diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5975d8b2..1238644b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,6 @@
 ## master / unreleased
  - [CHANGE] New `WALSegmentSize` option to override the `DefaultOptions.WALSegmentSize`. Added to allow using smaller wal files. For example using tmpfs on a RPI to minimise the SD card wear out from the constant WAL writes. As part of this change the `DefaultOptions.WALSegmentSize` constant was also exposed.
+ - [CHANGE] Empty blocks are not written during compaction [#374](https://github.com/prometheus/tsdb/pull/374)
  - [FEATURE]  Size base retention through `Options.MaxBytes`.  As part of this change:
     - added new metrics - `prometheus_tsdb_storage_blocks_bytes_total`, `prometheus_tsdb_size_retentions_total`, `prometheus_tsdb_time_retentions_total`
     - new public interface `SizeReader: Size() int64`
diff --git a/block.go b/block.go
index 837f4a76..42e11d95 100644
--- a/block.go
+++ b/block.go
@@ -191,6 +191,9 @@ type BlockMetaCompaction struct {
 	Level int `json:"level"`
 	// ULIDs of all source head blocks that went into the block.
 	Sources []ulid.ULID `json:"sources,omitempty"`
+	// Indicates that during compaction it resulted in a block without any samples
+	// so it should be deleted on the next reload.
+	Deletable bool `json:"deletable,omitempty"`
 	// Short descriptions of the direct blocks that were used to create
 	// this block.
 	Parents []BlockDesc `json:"parents,omitempty"`
diff --git a/block_test.go b/block_test.go
index 789aebaa..724ab378 100644
--- a/block_test.go
+++ b/block_test.go
@@ -45,7 +45,7 @@ func TestSetCompactionFailed(t *testing.T) {
 	testutil.Ok(t, err)
 	defer os.RemoveAll(tmpdir)
 
-	blockDir := createBlock(t, tmpdir, 0, 0, 0)
+	blockDir := createBlock(t, tmpdir, 1, 0, 0)
 	b, err := OpenBlock(nil, blockDir, nil)
 	testutil.Ok(t, err)
 	testutil.Equals(t, false, b.meta.Compaction.Failed)
@@ -91,6 +91,5 @@ func createBlock(tb testing.TB, dir string, nSeries int, mint, maxt int64) strin
 
 	ulid, err := compactor.Write(dir, head, head.MinTime(), head.MaxTime(), nil)
 	testutil.Ok(tb, err)
-
 	return filepath.Join(dir, ulid.String())
 }
diff --git a/compact.go b/compact.go
index 49d4e586..5d8155f5 100644
--- a/compact.go
+++ b/compact.go
@@ -55,12 +55,17 @@ type Compactor interface {
 	Plan(dir string) ([]string, error)
 
 	// Write persists a Block into a directory.
+	// No Block is written when resulting Block has 0 samples, and returns empty ulid.ULID{}.
 	Write(dest string, b BlockReader, mint, maxt int64, parent *BlockMeta) (ulid.ULID, error)
 
 	// Compact runs compaction against the provided directories. Must
 	// only be called concurrently with results of Plan().
 	// Can optionally pass a list of already open blocks,
 	// to avoid having to reopen them.
+	// When resulting Block has 0 samples
+	//  * No block is written.
+	//  * The source dirs are marked Deletable.
+	//  * Returns empty ulid.ULID{}.
 	Compact(dest string, dirs []string, open []*Block) (ulid.ULID, error)
 }
 
@@ -186,13 +191,12 @@ func (c *LeveledCompactor) plan(dms []dirMeta) ([]string, error) {
 		return res, nil
 	}
 
-	// Compact any blocks that have >5% tombstones.
+	// Compact any blocks with big enough time range that have >5% tombstones.
 	for i := len(dms) - 1; i >= 0; i-- {
 		meta := dms[i].meta
 		if meta.MaxTime-meta.MinTime < c.ranges[len(c.ranges)/2] {
 			break
 		}
-
 		if float64(meta.Stats.NumTombstones)/float64(meta.Stats.NumSeries+1) > 0.05 {
 			return []string{dms[i].dir}, nil
 		}
@@ -366,15 +370,34 @@ func (c *LeveledCompactor) Compact(dest string, dirs []string, open []*Block) (u
 	meta := compactBlockMetas(uid, metas...)
 	err = c.write(dest, meta, blocks...)
 	if err == nil {
-		level.Info(c.logger).Log(
-			"msg", "compact blocks",
-			"count", len(blocks),
-			"mint", meta.MinTime,
-			"maxt", meta.MaxTime,
-			"ulid", meta.ULID,
-			"sources", fmt.Sprintf("%v", uids),
-			"duration", time.Since(start),
-		)
+		if meta.Stats.NumSamples == 0 {
+			for _, b := range bs {
+				b.meta.Compaction.Deletable = true
+				if err = writeMetaFile(b.dir, &b.meta); err != nil {
+					level.Error(c.logger).Log(
+						"msg", "Failed to write 'Deletable' to meta file after compaction",
+						"ulid", b.meta.ULID,
+					)
+				}
+			}
+			uid = ulid.ULID{}
+			level.Info(c.logger).Log(
+				"msg", "compact blocks resulted in empty block",
+				"count", len(blocks),
+				"sources", fmt.Sprintf("%v", uids),
+				"duration", time.Since(start),
+			)
+		} else {
+			level.Info(c.logger).Log(
+				"msg", "compact blocks",
+				"count", len(blocks),
+				"mint", meta.MinTime,
+				"maxt", meta.MaxTime,
+				"ulid", meta.ULID,
+				"sources", fmt.Sprintf("%v", uids),
+				"duration", time.Since(start),
+			)
+		}
 		return uid, nil
 	}
 
@@ -413,6 +436,10 @@ func (c *LeveledCompactor) Write(dest string, b BlockReader, mint, maxt int64, p
 		return uid, err
 	}
 
+	if meta.Stats.NumSamples == 0 {
+		return ulid.ULID{}, nil
+	}
+
 	level.Info(c.logger).Log("msg", "write block", "mint", meta.MinTime, "maxt", meta.MaxTime, "ulid", meta.ULID)
 	return uid, nil
 }
@@ -490,11 +517,6 @@ func (c *LeveledCompactor) write(dest string, meta *BlockMeta, blocks ...BlockRe
 	if err := c.populateBlock(blocks, meta, indexw, chunkw); err != nil {
 		return errors.Wrap(err, "write compaction")
 	}
-
-	if err = writeMetaFile(tmp, meta); err != nil {
-		return errors.Wrap(err, "write merged meta")
-	}
-
 	// We are explicitly closing them here to check for error even
 	// though these are covered under defer. This is because in Windows,
 	// you cannot delete these unless they are closed and the defer is to
@@ -506,6 +528,18 @@ func (c *LeveledCompactor) write(dest string, meta *BlockMeta, blocks ...BlockRe
 		return errors.Wrap(err, "close index writer")
 	}
 
+	// Populated block is empty, so cleanup and exit.
+	if meta.Stats.NumSamples == 0 {
+		if err := os.RemoveAll(tmp); err != nil {
+			return errors.Wrap(err, "remove tmp folder after empty block failed")
+		}
+		return nil
+	}
+
+	if err = writeMetaFile(tmp, meta); err != nil {
+		return errors.Wrap(err, "write merged meta")
+	}
+
 	// Create an empty tombstones file.
 	if err := writeTombstoneFile(tmp, newMemTombstones()); err != nil {
 		return errors.Wrap(err, "write new tombstones file")
diff --git a/db.go b/db.go
index 63070043..1349dfbd 100644
--- a/db.go
+++ b/db.go
@@ -417,7 +417,8 @@ func (db *DB) compact() (err error) {
 			// from the block interval here.
 			maxt: maxt - 1,
 		}
-		if _, err = db.compactor.Write(db.dir, head, mint, maxt, nil); err != nil {
+		uid, err := db.compactor.Write(db.dir, head, mint, maxt, nil)
+		if err != nil {
 			return errors.Wrap(err, "persist head block")
 		}
 
@@ -426,6 +427,14 @@ func (db *DB) compact() (err error) {
 		if err := db.reload(); err != nil {
 			return errors.Wrap(err, "reload blocks")
 		}
+		if (uid == ulid.ULID{}) {
+			// Compaction resulted in an empty block.
+			// Head truncating during db.reload() depends on the persisted blocks and
+			// in this case no new block will be persisted so manually truncate the head.
+			if err = db.head.Truncate(maxt); err != nil {
+				return errors.Wrap(err, "head truncate failed (in compact)")
+			}
+		}
 		runtime.GC()
 	}
 
@@ -588,6 +597,12 @@ func (db *DB) deletableBlocks(blocks []*Block) map[ulid.ULID]*Block {
 		return blocks[i].Meta().MaxTime > blocks[j].Meta().MaxTime
 	})
 
+	for _, block := range blocks {
+		if block.Meta().Compaction.Deletable {
+			deletable[block.Meta().ULID] = block
+		}
+	}
+
 	for ulid, block := range db.beyondTimeRetention(blocks) {
 		deletable[ulid] = block
 	}
diff --git a/db_test.go b/db_test.go
index 2beef0c5..21de405e 100644
--- a/db_test.go
+++ b/db_test.go
@@ -836,7 +836,7 @@ func TestTombstoneCleanFail(t *testing.T) {
 	// totalBlocks should be >=2 so we have enough blocks to trigger compaction failure.
 	totalBlocks := 2
 	for i := 0; i < totalBlocks; i++ {
-		blockDir := createBlock(t, db.Dir(), 0, 0, 0)
+		blockDir := createBlock(t, db.Dir(), 1, 0, 0)
 		block, err := OpenBlock(nil, blockDir, nil)
 		testutil.Ok(t, err)
 		// Add some some fake tombstones to trigger the compaction.
@@ -880,7 +880,7 @@ func (c *mockCompactorFailing) Write(dest string, b BlockReader, mint, maxt int6
 		return ulid.ULID{}, fmt.Errorf("the compactor already did the maximum allowed blocks so it is time to fail")
 	}
 
-	block, err := OpenBlock(nil, createBlock(c.t, dest, 0, 0, 0), nil)
+	block, err := OpenBlock(nil, createBlock(c.t, dest, 1, 0, 0), nil)
 	testutil.Ok(c.t, err)
 	testutil.Ok(c.t, block.Close()) // Close block as we won't be using anywhere.
 	c.blocks = append(c.blocks, block)
@@ -1364,6 +1364,109 @@ func TestInitializeHeadTimestamp(t *testing.T) {
 	})
 }
 
+func TestNoEmptyBlocks(t *testing.T) {
+	db, close := openTestDB(t, &Options{
+		BlockRanges: []int64{100},
+	})
+	defer close()
+	defer db.Close()
+	db.DisableCompactions()
+
+	rangeToTriggercompaction := db.opts.BlockRanges[0]/2*3 - 1
+	defaultLabel := labels.FromStrings("foo", "bar")
+	defaultMatcher := labels.NewMustRegexpMatcher("", ".*")
+
+	t.Run("Test no blocks after compact with empty head.", func(t *testing.T) {
+		testutil.Ok(t, db.compact())
+		actBlocks, err := blockDirs(db.Dir())
+		testutil.Ok(t, err)
+		testutil.Equals(t, len(db.Blocks()), len(actBlocks))
+		testutil.Equals(t, 0, len(actBlocks))
+		testutil.Equals(t, 0, int(prom_testutil.ToFloat64(db.compactor.(*LeveledCompactor).metrics.ran)), "no compaction should be triggered here")
+	})
+
+	t.Run("Test no blocks after deleting all samples from head.", func(t *testing.T) {
+		app := db.Appender()
+		_, err := app.Add(defaultLabel, 1, 0)
+		testutil.Ok(t, err)
+		_, err = app.Add(defaultLabel, 2, 0)
+		testutil.Ok(t, err)
+		_, err = app.Add(defaultLabel, 3+rangeToTriggercompaction, 0)
+		testutil.Ok(t, err)
+		testutil.Ok(t, app.Commit())
+		testutil.Ok(t, db.Delete(math.MinInt64, math.MaxInt64, defaultMatcher))
+		testutil.Ok(t, db.compact())
+		testutil.Equals(t, 1, int(prom_testutil.ToFloat64(db.compactor.(*LeveledCompactor).metrics.ran)), "compaction should have been triggered here")
+
+		actBlocks, err := blockDirs(db.Dir())
+		testutil.Ok(t, err)
+		testutil.Equals(t, len(db.Blocks()), len(actBlocks))
+		testutil.Equals(t, 0, len(actBlocks))
+
+		app = db.Appender()
+		_, err = app.Add(defaultLabel, 1, 0)
+		testutil.Assert(t, err == ErrOutOfBounds, "the head should be truncated so no samples in the past should be allowed")
+
+		// Adding new blocks.
+		currentTime := db.Head().MaxTime()
+		_, err = app.Add(defaultLabel, currentTime, 0)
+		testutil.Ok(t, err)
+		_, err = app.Add(defaultLabel, currentTime+1, 0)
+		testutil.Ok(t, err)
+		_, err = app.Add(defaultLabel, currentTime+rangeToTriggercompaction, 0)
+		testutil.Ok(t, err)
+		testutil.Ok(t, app.Commit())
+
+		testutil.Ok(t, db.compact())
+		testutil.Equals(t, 2, int(prom_testutil.ToFloat64(db.compactor.(*LeveledCompactor).metrics.ran)), "compaction should have been triggered here")
+		actBlocks, err = blockDirs(db.Dir())
+		testutil.Ok(t, err)
+		testutil.Equals(t, len(db.Blocks()), len(actBlocks))
+		testutil.Assert(t, len(actBlocks) == 1, "No blocks created when compacting with >0 samples")
+	})
+
+	t.Run(`When no new block is created from head, and there are some blocks on disk 
+	compaction should not run into infinite loop (was seen during development).`, func(t *testing.T) {
+		oldBlocks := db.Blocks()
+		app := db.Appender()
+		currentTime := db.Head().MaxTime()
+		_, err := app.Add(defaultLabel, currentTime, 0)
+		testutil.Ok(t, err)
+		_, err = app.Add(defaultLabel, currentTime+1, 0)
+		testutil.Ok(t, err)
+		_, err = app.Add(defaultLabel, currentTime+rangeToTriggercompaction, 0)
+		testutil.Ok(t, err)
+		testutil.Ok(t, app.Commit())
+		testutil.Ok(t, db.head.Delete(math.MinInt64, math.MaxInt64, defaultMatcher))
+		testutil.Ok(t, db.compact())
+		testutil.Equals(t, 3, int(prom_testutil.ToFloat64(db.compactor.(*LeveledCompactor).metrics.ran)), "compaction should have been triggered here")
+		testutil.Equals(t, oldBlocks, db.Blocks())
+	})
+
+	t.Run("Test no blocks remaining after deleting all samples from disk.", func(t *testing.T) {
+		currentTime := db.Head().MaxTime()
+		blocks := []*BlockMeta{
+			{MinTime: currentTime, MaxTime: currentTime + db.opts.BlockRanges[0]},
+			{MinTime: currentTime + 100, MaxTime: currentTime + 100 + db.opts.BlockRanges[0]},
+		}
+		for _, m := range blocks {
+			createBlock(t, db.Dir(), 2, m.MinTime, m.MaxTime)
+		}
+
+		oldBlocks := db.Blocks()
+		testutil.Ok(t, db.reload())                                      // Reload the db to register the new blocks.
+		testutil.Equals(t, len(blocks)+len(oldBlocks), len(db.Blocks())) // Ensure all blocks are registered.
+		testutil.Ok(t, db.Delete(math.MinInt64, math.MaxInt64, defaultMatcher))
+		testutil.Ok(t, db.compact())
+		testutil.Equals(t, 5, int(prom_testutil.ToFloat64(db.compactor.(*LeveledCompactor).metrics.ran)), "compaction should have been triggered here once for each block that have tombstones")
+
+		actBlocks, err := blockDirs(db.Dir())
+		testutil.Ok(t, err)
+		testutil.Equals(t, len(db.Blocks()), len(actBlocks))
+		testutil.Equals(t, 1, len(actBlocks), "All samples are deleted. Only the most recent block should remain after compaction.")
+	})
+}
+
 func TestDB_LabelNames(t *testing.T) {
 	tests := []struct {
 		// Add 'sampleLabels1' -> Test Head -> Compact -> Test Disk ->
@@ -1468,12 +1571,13 @@ func TestCorrectNumTombstones(t *testing.T) {
 	defer db.Close()
 
 	blockRange := DefaultOptions.BlockRanges[0]
-	label := labels.FromStrings("foo", "bar")
+	defaultLabel := labels.FromStrings("foo", "bar")
+	defaultMatcher := labels.NewEqualMatcher(defaultLabel[0].Name, defaultLabel[0].Value)
 
 	app := db.Appender()
 	for i := int64(0); i < 3; i++ {
 		for j := int64(0); j < 15; j++ {
-			_, err := app.Add(label, i*blockRange+j, 0)
+			_, err := app.Add(defaultLabel, i*blockRange+j, 0)
 			testutil.Ok(t, err)
 		}
 	}
@@ -1483,17 +1587,17 @@ func TestCorrectNumTombstones(t *testing.T) {
 	testutil.Ok(t, err)
 	testutil.Equals(t, 1, len(db.blocks))
 
-	testutil.Ok(t, db.Delete(0, 1, labels.NewEqualMatcher("foo", "bar")))
+	testutil.Ok(t, db.Delete(0, 1, defaultMatcher))
 	testutil.Equals(t, uint64(1), db.blocks[0].meta.Stats.NumTombstones)
 
 	// {0, 1} and {2, 3} are merged to form 1 tombstone.
-	testutil.Ok(t, db.Delete(2, 3, labels.NewEqualMatcher("foo", "bar")))
+	testutil.Ok(t, db.Delete(2, 3, defaultMatcher))
 	testutil.Equals(t, uint64(1), db.blocks[0].meta.Stats.NumTombstones)
 
-	testutil.Ok(t, db.Delete(5, 6, labels.NewEqualMatcher("foo", "bar")))
+	testutil.Ok(t, db.Delete(5, 6, defaultMatcher))
 	testutil.Equals(t, uint64(2), db.blocks[0].meta.Stats.NumTombstones)
 
-	testutil.Ok(t, db.Delete(9, 11, labels.NewEqualMatcher("foo", "bar")))
+	testutil.Ok(t, db.Delete(9, 11, defaultMatcher))
 	testutil.Equals(t, uint64(3), db.blocks[0].meta.Stats.NumTombstones)
 }