diff --git a/chunks/chunk.go b/chunks/chunk.go
index 86f456be87..4eeb9c5d79 100644
--- a/chunks/chunk.go
+++ b/chunks/chunk.go
@@ -43,6 +43,7 @@ type Chunk interface {
 	Encoding() Encoding
 	Appender() (Appender, error)
 	Iterator() Iterator
+	NumSamples() int
 }
 
 // FromData returns a chunk from a byte slice of chunk data.
diff --git a/chunks/xor.go b/chunks/xor.go
index a72e9ef0cb..e9bdef0741 100644
--- a/chunks/xor.go
+++ b/chunks/xor.go
@@ -72,6 +72,11 @@ func (c *XORChunk) Bytes() []byte {
 	return c.b.bytes()
 }
 
+// NumSamples returns the number of samples in the chunk.
+func (c *XORChunk) NumSamples() int {
+	return int(binary.BigEndian.Uint16(c.Bytes()))
+}
+
 // Appender implements the Chunk interface.
 func (c *XORChunk) Appender() (Appender, error) {
 	it := c.iterator()
diff --git a/compact.go b/compact.go
index 6158f2d67a..1036cf4031 100644
--- a/compact.go
+++ b/compact.go
@@ -160,7 +160,24 @@ func (c *compactor) Plan() ([][]string, error) {
 		return [][]string{res}
 	}
 
-	return sliceDirs(c.selectDirs(dms)), nil
+	planDirs := sliceDirs(c.selectDirs(dms))
+	if len(dirs) > 1 {
+		return planDirs, nil
+	}
+
+	// Compact any blocks that have >5% tombstones.
+	for i := len(dms) - 1; i >= 0; i-- {
+		meta := dms[i].meta
+		if meta.MaxTime-meta.MinTime < c.opts.blockRanges[len(c.opts.blockRanges)/2] {
+			break
+		}
+
+		if meta.Stats.NumSeries/meta.Stats.NumTombstones <= 20 { // 5%
+			return [][]string{{dms[i].dir}}, nil
+		}
+	}
+
+	return nil, nil
 }
 
 func (c *compactor) selectDirs(ds []dirMeta) []dirMeta {
@@ -238,8 +255,6 @@ func compactBlockMetas(blocks ...BlockMeta) (res BlockMeta) {
 	sources := map[ulid.ULID]struct{}{}
 
 	for _, b := range blocks {
-		res.Stats.NumSamples += b.Stats.NumSamples
-
 		if b.Compaction.Generation > res.Compaction.Generation {
 			res.Compaction.Generation = b.Compaction.Generation
 		}
@@ -410,6 +425,11 @@ func populateBlock(blocks []Block, indexw IndexWriter, chunkw ChunkWriter) (*Blo
 	for set.Next() {
 		lset, chks, dranges := set.At() // The chunks here are not fully deleted.
 
+		// Skip the series with all deleted chunks.
+		if len(chks) == 0 {
+			continue
+		}
+
 		if len(dranges) > 0 {
 			// Re-encode the chunk to not have deleted values.
 			for _, chk := range chks {
@@ -439,6 +459,9 @@ func populateBlock(blocks []Block, indexw IndexWriter, chunkw ChunkWriter) (*Blo
 
 		meta.Stats.NumChunks += uint64(len(chks))
 		meta.Stats.NumSeries++
+		for _, chk := range chks {
+			meta.Stats.NumSamples += uint64(chk.Chunk.NumSamples())
+		}
 
 		for _, l := range lset {
 			valset, ok := values[l.Name]