diff --git a/block_test.go b/block_test.go
index 4ebb9685d..370047d5d 100644
--- a/block_test.go
+++ b/block_test.go
@@ -23,6 +23,21 @@ import (
 	"github.com/prometheus/tsdb/testutil"
 )
 
+// In Prometheus 2.1.0 we had a bug where the meta.json version was falsely bumped
+// to 2. We had a migration in place resetting it to 1 but we should move immediately to
+// version 3 next time to avoid confusion and issues.
+func TestBlockMetaMustNeverBeVersion2(t *testing.T) {
+	dir, err := ioutil.TempDir("", "metaversion")
+	testutil.Ok(t, err)
+	defer os.RemoveAll(dir)
+
+	testutil.Ok(t, writeMetaFile(dir, &BlockMeta{}))
+
+	meta, err := readMetaFile(dir)
+	testutil.Ok(t, err)
+	testutil.Assert(t, meta.Version != 2, "meta.json version must never be 2")
+}
+
 func TestSetCompactionFailed(t *testing.T) {
 	tmpdir, err := ioutil.TempDir("", "test-tsdb")
 	testutil.Ok(t, err)
diff --git a/db.go b/db.go
index 6490c01df..1ac2d425f 100644
--- a/db.go
+++ b/db.go
@@ -188,6 +188,7 @@ func Open(dir string, l log.Logger, r prometheus.Registerer, opts *Options) (db
 	if opts == nil {
 		opts = DefaultOptions
 	}
+	// Fixup bad format written by Prometheus 2.1.
 	if err := repairBadIndexVersion(l, dir); err != nil {
 		return nil, err
 	}
diff --git a/index/index.go b/index/index.go
index 4fdc0398c..146332d10 100644
--- a/index/index.go
+++ b/index/index.go
@@ -136,7 +136,7 @@ type indexTOC struct {
 	postingsTable     uint64
 }
 
-// NewWriter returns a new Writer to the given filename.
+// NewWriter returns a new Writer to the given filename. It serializes data in format version 2.
 func NewWriter(fn string) (*Writer, error) {
 	dir := filepath.Dir(fn)
 
@@ -577,7 +577,8 @@ func (b realByteSlice) Sub(start, end int) ByteSlice {
 	return b[start:end]
 }
 
-// NewReader returns a new IndexReader on the given byte slice.
+// NewReader returns a new IndexReader on the given byte slice. It automatically
+// handles different format versions.
 func NewReader(b ByteSlice) (*Reader, error) {
 	return newReader(b, nil)
 }
diff --git a/repair.go b/repair.go
index 61ec4bb8c..e9f2a9643 100644
--- a/repair.go
+++ b/repair.go
@@ -15,6 +15,8 @@ import (
 	"github.com/prometheus/tsdb/fileutil"
 )
 
+// repairBadIndexVersion repairs an issue in index and meta.json persistence introduced in
+// commit 129773b41a565fde5156301e37f9a87158030443.
 func repairBadIndexVersion(logger log.Logger, dir string) error {
 	// All blocks written by Prometheus 2.1 with a meta.json version of 2 are affected.
 	// We must actually set the index file version to 2 and revert the meta.json version back to 1.
diff --git a/repair_test.go b/repair_test.go
index e133bceab..f4c9d2087 100644
--- a/repair_test.go
+++ b/repair_test.go
@@ -1,12 +1,12 @@
 package tsdb
 
 import (
+	"os"
 	"reflect"
 	"testing"
 
 	"github.com/prometheus/tsdb/chunks"
 
-	"github.com/go-kit/kit/log"
 	"github.com/prometheus/tsdb/index"
 	"github.com/prometheus/tsdb/labels"
 )
@@ -52,6 +52,8 @@ func TestRepairBadIndexVersion(t *testing.T) {
 	if err == nil {
 		t.Fatal("error expected but got none")
 	}
+	// Touch chunks dir in block.
+	os.MkdirAll(dir+"chunks", 0777)
 
 	r, err := index.NewFileReader(dir + "index")
 	if err != nil {
@@ -73,9 +75,12 @@ func TestRepairBadIndexVersion(t *testing.T) {
 		t.Fatal(err)
 	}
 
-	if err := repairBadIndexVersion(log.NewNopLogger(), "testdata/repair_index_version"); err != nil {
+	// On DB opening all blocks in the base dir should be repaired.
+	db, _ := Open("testdata/repair_index_version", nil, nil, nil)
+	if err != nil {
 		t.Fatal(err)
 	}
+	db.Close()
 
 	r, err = index.NewFileReader(dir + "index")
 	if err != nil {