diff --git a/block.go b/block.go
index 400cdac786..2dab0c32d5 100644
--- a/block.go
+++ b/block.go
@@ -151,6 +151,9 @@ type BlockMeta struct {
 
 	// Information on compactions the block was created from.
 	Compaction BlockMetaCompaction `json:"compaction"`
+
+	// Version of the index format.
+	Version int `json:"version"`
 }
 
 // BlockStats contains stats about contents of a block.
@@ -176,12 +179,6 @@ const (
 	flagStd  = 1
 )
 
-type blockMeta struct {
-	Version int `json:"version"`
-
-	*BlockMeta
-}
-
 const indexFilename = "index"
 const metaFilename = "meta.json"
 
@@ -193,16 +190,16 @@ func readMetaFile(dir string) (*BlockMeta, error) {
 	if err != nil {
 		return nil, err
 	}
-	var m blockMeta
+	var m BlockMeta
 
 	if err := json.Unmarshal(b, &m); err != nil {
 		return nil, err
 	}
-	if m.Version != 1 {
+	if m.Version != 1 && m.Version != 2 {
 		return nil, errors.Errorf("unexpected meta file version %d", m.Version)
 	}
 
-	return m.BlockMeta, nil
+	return &m, nil
 }
 
 func writeMetaFile(dir string, meta *BlockMeta) error {
@@ -219,7 +216,8 @@ func writeMetaFile(dir string, meta *BlockMeta) error {
 	enc.SetIndent("", "\t")
 
 	var merr MultiError
-	if merr.Add(enc.Encode(&blockMeta{Version: 1, BlockMeta: meta})); merr.Err() != nil {
+
+	if merr.Add(enc.Encode(meta)); merr.Err() != nil {
 		merr.Add(f.Close())
 		return merr.Err()
 	}
@@ -255,7 +253,7 @@ func OpenBlock(dir string, pool chunkenc.Pool) (*Block, error) {
 	if err != nil {
 		return nil, err
 	}
-	ir, err := index.NewFileReader(filepath.Join(dir, "index"))
+	ir, err := index.NewFileReader(filepath.Join(dir, "index"), meta.Version)
 	if err != nil {
 		return nil, err
 	}
diff --git a/block_test.go b/block_test.go
index 690cd07ad1..4ebb9685d0 100644
--- a/block_test.go
+++ b/block_test.go
@@ -42,7 +42,7 @@ func TestSetCompactionFailed(t *testing.T) {
 func createEmptyBlock(t *testing.T, dir string) *Block {
 	testutil.Ok(t, os.MkdirAll(dir, 0777))
 
-	testutil.Ok(t, writeMetaFile(dir, &BlockMeta{}))
+	testutil.Ok(t, writeMetaFile(dir, &BlockMeta{Version: 2}))
 
 	ir, err := index.NewWriter(filepath.Join(dir, indexFilename))
 	testutil.Ok(t, err)
diff --git a/compact.go b/compact.go
index 5c532759f9..f96e643945 100644
--- a/compact.go
+++ b/compact.go
@@ -428,6 +428,7 @@ func (c *LeveledCompactor) write(dest string, meta *BlockMeta, blocks ...BlockRe
 	}
 
 	indexw, err := index.NewWriter(filepath.Join(tmp, indexFilename))
+	meta.Version = indexw.Version
 	if err != nil {
 		return errors.Wrap(err, "open index writer")
 	}
diff --git a/Documentation/format/chunks.md b/docs/format/chunks.md
similarity index 100%
rename from Documentation/format/chunks.md
rename to docs/format/chunks.md
diff --git a/Documentation/format/index.md b/docs/format/index.md
similarity index 98%
rename from Documentation/format/index.md
rename to docs/format/index.md
index ce37999078..48366ef8dd 100644
--- a/Documentation/format/index.md
+++ b/docs/format/index.md
@@ -65,7 +65,7 @@ Strings are referenced by pointing to the beginning of their length field. The s
 ### Series
 
 The section contains a sequence of series that hold the label set of the series as well as its chunks within the block. The series are sorted lexicographically by their label sets.  
-The file offset to the beginning of a series serves as the series' ID in all subsequent references. Thereby, a sorted list of series IDs implies a lexicographically sorted list of series label sets.
+Each series section is aligned to 16 bytes. The ID for a series is the `offset/16`. This serves as the series' ID in all subsequent references. Thereby, a sorted list of series IDs implies a lexicographically sorted list of series label sets. 
 
 ```
 ┌───────────────────────────────────────┐
diff --git a/Documentation/format/tombstones.md b/docs/format/tombstones.md
similarity index 100%
rename from Documentation/format/tombstones.md
rename to docs/format/tombstones.md
diff --git a/index/index.go b/index/index.go
index ad6dbb218a..df8d7b5fea 100644
--- a/index/index.go
+++ b/index/index.go
@@ -98,7 +98,7 @@ func newCRC32() hash.Hash32 {
 	return crc32.New(castagnoliTable)
 }
 
-// indexWriter implements the IndexWriter interface for the standard
+// Writer implements the IndexWriter interface for the standard
 // serialization format.
 type Writer struct {
 	f    *os.File
@@ -122,6 +122,8 @@ type Writer struct {
 	lastSeries labels.Labels
 
 	crc32 hash.Hash
+
+	Version int
 }
 
 type indexTOC struct {
@@ -166,6 +168,8 @@ func NewWriter(fn string) (*Writer, error) {
 		symbols:       make(map[string]uint32, 1<<13),
 		seriesOffsets: make(map[uint64]uint64, 1<<16),
 		crc32:         newCRC32(),
+
+		Version: 2,
 	}
 	if err := iw.writeMeta(); err != nil {
 		return nil, err
@@ -180,12 +184,12 @@ func (w *Writer) write(bufs ...[]byte) error {
 		if err != nil {
 			return err
 		}
-		// For now the index file must not grow beyond 4GiB. Some of the fixed-sized
+		// For now the index file must not grow beyond 64GiB. Some of the fixed-sized
 		// offset references in v1 are only 4 bytes large.
 		// Once we move to compressed/varint representations in those areas, this limitation
 		// can be lifted.
-		if w.pos > math.MaxUint32 {
-			return errors.Errorf("exceeding max size of 4GiB")
+		if w.pos > 16*math.MaxUint32 {
+			return errors.Errorf("exceeding max size of 64GiB")
 		}
 	}
 	return nil
@@ -250,6 +254,7 @@ func (w *Writer) writeMeta() error {
 	return w.write(w.buf1.get())
 }
 
+// AddSeries adds the series one at a time along with its chunks.
 func (w *Writer) AddSeries(ref uint64, lset labels.Labels, chunks ...chunks.Meta) error {
 	if err := w.ensureStage(idxStageSeries); err != nil {
 		return err
@@ -261,7 +266,8 @@ func (w *Writer) AddSeries(ref uint64, lset labels.Labels, chunks ...chunks.Meta
 	if _, ok := w.seriesOffsets[ref]; ok {
 		return errors.Errorf("series with reference %d already added", ref)
 	}
-	w.seriesOffsets[ref] = w.pos
+	w.addPadding(16)
+	w.seriesOffsets[ref] = w.pos / 16
 
 	w.buf2.reset()
 	w.buf2.putUvarint(len(lset))
@@ -531,9 +537,11 @@ type Reader struct {
 	// the block has been unmapped.
 	symbols map[uint32]string
 
-	dec *DecoderV1
+	dec *Decoder
 
 	crc32 hash.Hash32
+
+	version int
 }
 
 var (
@@ -563,20 +571,20 @@ func (b realByteSlice) Sub(start, end int) ByteSlice {
 }
 
 // NewReader returns a new IndexReader on the given byte slice.
-func NewReader(b ByteSlice) (*Reader, error) {
-	return newReader(b, nil)
+func NewReader(b ByteSlice, version int) (*Reader, error) {
+	return newReader(b, nil, version)
 }
 
 // NewFileReader returns a new index reader against the given index file.
-func NewFileReader(path string) (*Reader, error) {
+func NewFileReader(path string, version int) (*Reader, error) {
 	f, err := fileutil.OpenMmapFile(path)
 	if err != nil {
 		return nil, err
 	}
-	return newReader(realByteSlice(f.Bytes()), f)
+	return newReader(realByteSlice(f.Bytes()), f, version)
 }
 
-func newReader(b ByteSlice, c io.Closer) (*Reader, error) {
+func newReader(b ByteSlice, c io.Closer, version int) (*Reader, error) {
 	r := &Reader{
 		b:        b,
 		c:        c,
@@ -584,6 +592,12 @@ func newReader(b ByteSlice, c io.Closer) (*Reader, error) {
 		labels:   map[string]uint32{},
 		postings: map[labels.Label]uint32{},
 		crc32:    newCRC32(),
+		version:  version,
+	}
+
+	if version != 1 && version != 2 {
+		return nil, errors.Errorf("unexpected file version %d", version)
+
 	}
 	// Verify magic number.
 	if b.Len() < 4 {
@@ -622,7 +636,7 @@ func newReader(b ByteSlice, c io.Closer) (*Reader, error) {
 		return nil, errors.Wrap(err, "read postings table")
 	}
 
-	r.dec = &DecoderV1{symbols: r.symbols}
+	r.dec = &Decoder{symbols: r.symbols}
 
 	return r, nil
 }
@@ -852,9 +866,13 @@ func (r *Reader) LabelIndices() ([][]string, error) {
 	return res, nil
 }
 
-// Series the series with the given ID and writes its labels and chunks into lbls and chks.
+// Series reads the series with the given ID and writes its labels and chunks into lbls and chks.
 func (r *Reader) Series(id uint64, lbls *labels.Labels, chks *[]chunks.Meta) error {
-	d := r.decbufUvarintAt(int(id))
+	offset := id
+	if r.version == 2 {
+		offset = 16 * id
+	}
+	d := r.decbufUvarintAt(int(offset))
 	if d.err() != nil {
 		return d.err()
 	}
@@ -955,15 +973,15 @@ func (t *serializedStringTuples) At(i int) ([]string, error) {
 	return res, nil
 }
 
-// DecoderV1 provides decoding methods for the v1 index file format.
+// Decoder provides decoding methods for the v1 and v2 index file format.
 //
 // It currently does not contain decoding methods for all entry types but can be extended
 // by them if there's demand.
-type DecoderV1 struct {
+type Decoder struct {
 	symbols map[uint32]string
 }
 
-func (dec *DecoderV1) lookupSymbol(o uint32) (string, error) {
+func (dec *Decoder) lookupSymbol(o uint32) (string, error) {
 	s, ok := dec.symbols[o]
 	if !ok {
 		return "", errors.Errorf("unknown symbol offset %d", o)
@@ -973,12 +991,12 @@ func (dec *DecoderV1) lookupSymbol(o uint32) (string, error) {
 
 // SetSymbolTable set the symbol table to be used for lookups when decoding series
 // and label indices
-func (dec *DecoderV1) SetSymbolTable(t map[uint32]string) {
+func (dec *Decoder) SetSymbolTable(t map[uint32]string) {
 	dec.symbols = t
 }
 
 // Postings returns a postings list for b and its number of elements.
-func (dec *DecoderV1) Postings(b []byte) (int, Postings, error) {
+func (dec *Decoder) Postings(b []byte) (int, Postings, error) {
 	d := decbuf{b: b}
 	n := d.be32int()
 	l := d.get()
@@ -986,7 +1004,7 @@ func (dec *DecoderV1) Postings(b []byte) (int, Postings, error) {
 }
 
 // Series decodes a series entry from the given byte slice into lset and chks.
-func (dec *DecoderV1) Series(b []byte, lbls *labels.Labels, chks *[]chunks.Meta) error {
+func (dec *Decoder) Series(b []byte, lbls *labels.Labels, chks *[]chunks.Meta) error {
 	*lbls = (*lbls)[:0]
 	*chks = (*chks)[:0]
 
diff --git a/index/index_test.go b/index/index_test.go
index 83b6ef6574..65ef9b6e67 100644
--- a/index/index_test.go
+++ b/index/index_test.go
@@ -160,7 +160,7 @@ func TestIndexRW_Create_Open(t *testing.T) {
 	testutil.Ok(t, err)
 	testutil.Ok(t, iw.Close())
 
-	ir, err := NewFileReader(fn)
+	ir, err := NewFileReader(fn, 1)
 	testutil.Ok(t, err)
 	testutil.Ok(t, ir.Close())
 
@@ -170,7 +170,7 @@ func TestIndexRW_Create_Open(t *testing.T) {
 	_, err = f.WriteAt([]byte{0, 0}, 0)
 	testutil.Ok(t, err)
 
-	_, err = NewFileReader(dir)
+	_, err = NewFileReader(dir, 1)
 	testutil.NotOk(t, err)
 }
 
@@ -213,7 +213,7 @@ func TestIndexRW_Postings(t *testing.T) {
 
 	testutil.Ok(t, iw.Close())
 
-	ir, err := NewFileReader(fn)
+	ir, err := NewFileReader(fn, 2)
 	testutil.Ok(t, err)
 
 	p, err := ir.Postings("a", "1")
@@ -331,7 +331,7 @@ func TestPersistence_index_e2e(t *testing.T) {
 	err = iw.Close()
 	testutil.Ok(t, err)
 
-	ir, err := NewFileReader(filepath.Join(dir, "index"))
+	ir, err := NewFileReader(filepath.Join(dir, "index"), 2)
 	testutil.Ok(t, err)
 
 	for p := range mi.postings {