diff --git a/compact.go b/compact.go
index 3f5fa367c..0439ca310 100644
--- a/compact.go
+++ b/compact.go
@@ -524,6 +524,10 @@ func (c *LeveledCompactor) write(dest string, meta *BlockMeta, blocks ...BlockRe
 // populateBlock fills the index and chunk writers with new data gathered as the union
 // of the provided blocks. It returns meta information for the new block.
 func (c *LeveledCompactor) populateBlock(blocks []BlockReader, meta *BlockMeta, indexw IndexWriter, chunkw ChunkWriter) error {
+	if len(blocks) == 0 {
+		return errors.New("cannot populate block from no readers")
+	}
+
 	var (
 		set        ChunkSeriesSet
 		allSymbols = make(map[string]struct{}, 1<<16)
@@ -595,13 +599,17 @@ func (c *LeveledCompactor) populateBlock(blocks []BlockReader, meta *BlockMeta,
 			continue
 		}
 
-		if len(dranges) > 0 {
-			// Re-encode the chunk to not have deleted values.
-			for i, chk := range chks {
+		for i, chk := range chks {
+			if chk.MinTime < meta.MinTime || chk.MaxTime > meta.MaxTime {
+				return errors.Errorf("found chunk with minTime: %d maxTime: %d outside of compacted minTime: %d maxTime: %d",
+					chk.MinTime, chk.MaxTime, meta.MinTime, meta.MaxTime)
+			}
+
+			if len(dranges) > 0 {
+				// Re-encode the chunk to not have deleted values.
 				if !chk.OverlapsClosedInterval(dranges[0].Mint, dranges[len(dranges)-1].Maxt) {
 					continue
 				}
-
 				newChunk := chunkenc.NewXORChunk()
 				app, err := newChunk.Appender()
 				if err != nil {
@@ -617,6 +625,7 @@ func (c *LeveledCompactor) populateBlock(blocks []BlockReader, meta *BlockMeta,
 				chks[i].Chunk = newChunk
 			}
 		}
+
 		if err := chunkw.WriteChunks(chks...); err != nil {
 			return errors.Wrap(err, "write chunks")
 		}
@@ -791,7 +800,6 @@ func (c *compactionMerger) Next() bool {
 	var chks []chunks.Meta
 
 	d := c.compare()
-	// Both sets contain the current series. Chain them into a single one.
 	if d > 0 {
 		lset, chks, c.intervals = c.b.At()
 		c.l = append(c.l[:0], lset...)
@@ -805,8 +813,10 @@ func (c *compactionMerger) Next() bool {
 
 		c.aok = c.a.Next()
 	} else {
+		// Both sets contain the current series. Chain them into a single one.
 		l, ca, ra := c.a.At()
 		_, cb, rb := c.b.At()
+
 		for _, r := range rb {
 			ra = ra.add(r)
 		}
diff --git a/compact_test.go b/compact_test.go
index 42e38b5c6..acbbb5182 100644
--- a/compact_test.go
+++ b/compact_test.go
@@ -15,12 +15,14 @@ package tsdb
 
 import (
 	"io/ioutil"
+	"math"
 	"os"
 	"path/filepath"
 	"testing"
 
 	"github.com/go-kit/kit/log"
 	"github.com/pkg/errors"
+	"github.com/prometheus/tsdb/chunks"
 	"github.com/prometheus/tsdb/testutil"
 )
 
@@ -401,3 +403,282 @@ type erringBReader struct{}
 func (erringBReader) Index() (IndexReader, error)          { return nil, errors.New("index") }
 func (erringBReader) Chunks() (ChunkReader, error)         { return nil, errors.New("chunks") }
 func (erringBReader) Tombstones() (TombstoneReader, error) { return nil, errors.New("tombstones") }
+
+type nopChunkWriter struct{}
+
+func (nopChunkWriter) WriteChunks(chunks ...chunks.Meta) error { return nil }
+func (nopChunkWriter) Close() error                            { return nil }
+
+func TestCompaction_populateBlock(t *testing.T) {
+	var populateBlocksCases = []struct {
+		title              string
+		inputSeriesSamples [][]seriesSamples
+		compactMinTime     int64
+		compactMaxTime     int64 // When not defined the test runner sets a default of math.MaxInt64.
+
+		expSeriesSamples []seriesSamples
+		expErr           error
+	}{
+		{
+			title:              "Populate block from empty input should return error.",
+			inputSeriesSamples: [][]seriesSamples{},
+			expErr:             errors.New("cannot populate block from no readers"),
+		},
+		{
+			// Populate from single block without chunks. We expect these kind of series being ignored.
+			inputSeriesSamples: [][]seriesSamples{
+				{
+					{
+						lset: map[string]string{"a": "b"},
+					},
+				},
+			},
+		},
+		{
+			title: "Populate from single block. We expect the same samples at the output.",
+			inputSeriesSamples: [][]seriesSamples{
+				{
+					{
+						lset:   map[string]string{"a": "b"},
+						chunks: [][]sample{{{t: 0}, {t: 10}}, {{t: 11}, {t: 20}}},
+					},
+				},
+			},
+			expSeriesSamples: []seriesSamples{
+				{
+					lset:   map[string]string{"a": "b"},
+					chunks: [][]sample{{{t: 0}, {t: 10}}, {{t: 11}, {t: 20}}},
+				},
+			},
+		},
+		{
+			title: "Populate from two blocks.",
+			inputSeriesSamples: [][]seriesSamples{
+				{
+					{
+						lset:   map[string]string{"a": "b"},
+						chunks: [][]sample{{{t: 0}, {t: 10}}, {{t: 11}, {t: 20}}},
+					},
+					{
+						lset:   map[string]string{"a": "c"},
+						chunks: [][]sample{{{t: 1}, {t: 9}}, {{t: 10}, {t: 19}}},
+					},
+					{
+						// no-chunk series should be dropped.
+						lset: map[string]string{"a": "empty"},
+					},
+				},
+				{
+					{
+						lset:   map[string]string{"a": "b"},
+						chunks: [][]sample{{{t: 21}, {t: 30}}},
+					},
+					{
+						lset:   map[string]string{"a": "c"},
+						chunks: [][]sample{{{t: 40}, {t: 45}}},
+					},
+				},
+			},
+			expSeriesSamples: []seriesSamples{
+				{
+					lset:   map[string]string{"a": "b"},
+					chunks: [][]sample{{{t: 0}, {t: 10}}, {{t: 11}, {t: 20}}, {{t: 21}, {t: 30}}},
+				},
+				{
+					lset:   map[string]string{"a": "c"},
+					chunks: [][]sample{{{t: 1}, {t: 9}}, {{t: 10}, {t: 19}}, {{t: 40}, {t: 45}}},
+				},
+			},
+		},
+		{
+			title: "Populate from two blocks showing that order is maintained.",
+			inputSeriesSamples: [][]seriesSamples{
+				{
+					{
+						lset:   map[string]string{"a": "b"},
+						chunks: [][]sample{{{t: 21}, {t: 30}}},
+					},
+					{
+						lset:   map[string]string{"a": "c"},
+						chunks: [][]sample{{{t: 40}, {t: 45}}},
+					},
+				},
+				{
+					{
+						lset:   map[string]string{"a": "b"},
+						chunks: [][]sample{{{t: 0}, {t: 10}}, {{t: 11}, {t: 20}}},
+					},
+					{
+						lset:   map[string]string{"a": "c"},
+						chunks: [][]sample{{{t: 1}, {t: 9}}, {{t: 10}, {t: 19}}},
+					},
+				},
+			},
+			expSeriesSamples: []seriesSamples{
+				{
+					lset:   map[string]string{"a": "b"},
+					chunks: [][]sample{{{t: 21}, {t: 30}}, {{t: 0}, {t: 10}}, {{t: 11}, {t: 20}}},
+				},
+				{
+					lset:   map[string]string{"a": "c"},
+					chunks: [][]sample{{{t: 40}, {t: 45}}, {{t: 1}, {t: 9}}, {{t: 10}, {t: 19}}},
+				},
+			},
+		},
+		{
+			title: "Populate from two blocks showing that order or series is sorted.",
+			inputSeriesSamples: [][]seriesSamples{
+				{
+					{
+						lset:   map[string]string{"a": "4"},
+						chunks: [][]sample{{{t: 5}, {t: 7}}},
+					},
+					{
+						lset:   map[string]string{"a": "3"},
+						chunks: [][]sample{{{t: 5}, {t: 6}}},
+					},
+					{
+						lset:   map[string]string{"a": "same"},
+						chunks: [][]sample{{{t: 1}, {t: 4}}},
+					},
+				},
+				{
+					{
+						lset:   map[string]string{"a": "2"},
+						chunks: [][]sample{{{t: 1}, {t: 3}}},
+					},
+					{
+						lset:   map[string]string{"a": "1"},
+						chunks: [][]sample{{{t: 1}, {t: 2}}},
+					},
+					{
+						lset:   map[string]string{"a": "same"},
+						chunks: [][]sample{{{t: 5}, {t: 8}}},
+					},
+				},
+			},
+			expSeriesSamples: []seriesSamples{
+				{
+					lset:   map[string]string{"a": "1"},
+					chunks: [][]sample{{{t: 1}, {t: 2}}},
+				},
+				{
+					lset:   map[string]string{"a": "2"},
+					chunks: [][]sample{{{t: 1}, {t: 3}}},
+				},
+				{
+					lset:   map[string]string{"a": "3"},
+					chunks: [][]sample{{{t: 5}, {t: 6}}},
+				},
+				{
+					lset:   map[string]string{"a": "4"},
+					chunks: [][]sample{{{t: 5}, {t: 7}}},
+				},
+				{
+					lset:   map[string]string{"a": "same"},
+					chunks: [][]sample{{{t: 1}, {t: 4}}, {{t: 5}, {t: 8}}},
+				},
+			},
+		},
+		{
+			// This should not happened because head block is making sure the chunks are not crossing block boundaries.
+			title: "Populate from single block containing chunk outside of compact meta time range.",
+			inputSeriesSamples: [][]seriesSamples{
+				{
+					{
+						lset:   map[string]string{"a": "b"},
+						chunks: [][]sample{{{t: 1}, {t: 2}}, {{t: 10}, {t: 30}}},
+					},
+				},
+			},
+			compactMinTime: 0,
+			compactMaxTime: 20,
+			expErr:         errors.New("found chunk with minTime: 10 maxTime: 30 outside of compacted minTime: 0 maxTime: 20"),
+		},
+		{
+			// Introduced by https://github.com/prometheus/tsdb/issues/347.
+			title: "Populate from single block containing extra chunk",
+			inputSeriesSamples: [][]seriesSamples{
+				{
+					{
+						lset:   map[string]string{"a": "issue347"},
+						chunks: [][]sample{{{t: 1}, {t: 2}}, {{t: 10}, {t: 20}}},
+					},
+				},
+			},
+			compactMinTime: 0,
+			compactMaxTime: 10,
+			expErr:         errors.New("found chunk with minTime: 10 maxTime: 20 outside of compacted minTime: 0 maxTime: 10"),
+		},
+		{
+			// No special deduplication expected.
+			title: "Populate from two blocks containing duplicated chunk.",
+			inputSeriesSamples: [][]seriesSamples{
+				{
+					{
+						lset:   map[string]string{"a": "b"},
+						chunks: [][]sample{{{t: 1}, {t: 2}}, {{t: 10}, {t: 20}}},
+					},
+				},
+				{
+					{
+						lset:   map[string]string{"a": "b"},
+						chunks: [][]sample{{{t: 10}, {t: 20}}},
+					},
+				},
+			},
+			expSeriesSamples: []seriesSamples{
+				{
+					lset:   map[string]string{"a": "b"},
+					chunks: [][]sample{{{t: 1}, {t: 2}}, {{t: 10}, {t: 20}}, {{t: 10}, {t: 20}}},
+				},
+			},
+		},
+	}
+
+	for _, tc := range populateBlocksCases {
+		if ok := t.Run(tc.title, func(t *testing.T) {
+			blocks := make([]BlockReader, 0, len(tc.inputSeriesSamples))
+			for _, b := range tc.inputSeriesSamples {
+				ir, cr := createIdxChkReaders(b)
+				blocks = append(blocks, &mockBReader{ir: ir, cr: cr})
+			}
+
+			c, err := NewLeveledCompactor(nil, nil, []int64{0}, nil)
+			testutil.Ok(t, err)
+
+			meta := &BlockMeta{
+				MinTime: tc.compactMinTime,
+				MaxTime: tc.compactMaxTime,
+			}
+			if meta.MaxTime == 0 {
+				meta.MaxTime = math.MaxInt64
+			}
+
+			iw := &mockIndexWriter{}
+			err = c.populateBlock(blocks, meta, iw, nopChunkWriter{})
+			if tc.expErr != nil {
+				testutil.NotOk(t, err)
+				testutil.Equals(t, tc.expErr.Error(), err.Error())
+				return
+			}
+			testutil.Ok(t, err)
+
+			testutil.Equals(t, tc.expSeriesSamples, iw.series)
+
+			// Check if stats are calculated properly.
+			s := BlockStats{
+				NumSeries: uint64(len(tc.expSeriesSamples)),
+			}
+			for _, series := range tc.expSeriesSamples {
+				s.NumChunks += uint64(len(series.chunks))
+				for _, chk := range series.chunks {
+					s.NumSamples += uint64(len(chk))
+				}
+			}
+			testutil.Equals(t, s, meta.Stats)
+		}); !ok {
+			return
+		}
+	}
+}
diff --git a/mocks_test.go b/mocks_test.go
new file mode 100644
index 000000000..ab796f8b5
--- /dev/null
+++ b/mocks_test.go
@@ -0,0 +1,73 @@
+// Copyright 2017 The Prometheus Authors
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package tsdb
+
+import (
+	"github.com/prometheus/tsdb/chunks"
+	"github.com/prometheus/tsdb/index"
+	"github.com/prometheus/tsdb/labels"
+)
+
+type mockIndexWriter struct {
+	series []seriesSamples
+}
+
+func (mockIndexWriter) AddSymbols(sym map[string]struct{}) error { return nil }
+func (m *mockIndexWriter) AddSeries(ref uint64, l labels.Labels, chunks ...chunks.Meta) error {
+	i := -1
+	for j, s := range m.series {
+		if !labels.FromMap(s.lset).Equals(l) {
+			continue
+		}
+		i = j
+		break
+	}
+	if i == -1 {
+		m.series = append(m.series, seriesSamples{
+			lset: l.Map(),
+		})
+		i = len(m.series) - 1
+	}
+
+	for _, chk := range chunks {
+		samples := make([]sample, 0, chk.Chunk.NumSamples())
+
+		iter := chk.Chunk.Iterator()
+		for iter.Next() {
+			s := sample{}
+			s.t, s.v = iter.At()
+
+			samples = append(samples, s)
+		}
+		if err := iter.Err(); err != nil {
+			return err
+		}
+
+		m.series[i].chunks = append(m.series[i].chunks, samples)
+	}
+	return nil
+}
+
+func (mockIndexWriter) WriteLabelIndex(names []string, values []string) error     { return nil }
+func (mockIndexWriter) WritePostings(name, value string, it index.Postings) error { return nil }
+func (mockIndexWriter) Close() error                                              { return nil }
+
+type mockBReader struct {
+	ir IndexReader
+	cr ChunkReader
+}
+
+func (r *mockBReader) Index() (IndexReader, error)          { return r.ir, nil }
+func (r *mockBReader) Chunks() (ChunkReader, error)         { return r.cr, nil }
+func (r *mockBReader) Tombstones() (TombstoneReader, error) { return NewMemTombstones(), nil }
diff --git a/querier_test.go b/querier_test.go
index 87a45b647..1beaf8044 100644
--- a/querier_test.go
+++ b/querier_test.go
@@ -245,12 +245,14 @@ func expandSeriesIterator(it SeriesIterator) (r []sample, err error) {
 	return r, it.Err()
 }
 
-// Index: labels -> postings -> chunkMetas -> chunkRef
-// ChunkReader: ref -> vals
-func createIdxChkReaders(tc []struct {
+type seriesSamples struct {
 	lset   map[string]string
 	chunks [][]sample
-}) (IndexReader, ChunkReader) {
+}
+
+// Index: labels -> postings -> chunkMetas -> chunkRef
+// ChunkReader: ref -> vals
+func createIdxChkReaders(tc []seriesSamples) (IndexReader, ChunkReader) {
 	sort.Slice(tc, func(i, j int) bool {
 		return labels.Compare(labels.FromMap(tc[i].lset), labels.FromMap(tc[i].lset)) < 0
 	})
@@ -322,17 +324,11 @@ func TestBlockQuerier(t *testing.T) {
 	}
 
 	cases := struct {
-		data []struct {
-			lset   map[string]string
-			chunks [][]sample
-		}
+		data []seriesSamples
 
 		queries []query
 	}{
-		data: []struct {
-			lset   map[string]string
-			chunks [][]sample
-		}{
+		data: []seriesSamples{
 			{
 				lset: map[string]string{
 					"a": "a",
@@ -528,18 +524,12 @@ func TestBlockQuerierDelete(t *testing.T) {
 	}
 
 	cases := struct {
-		data []struct {
-			lset   map[string]string
-			chunks [][]sample
-		}
+		data []seriesSamples
 
 		tombstones TombstoneReader
 		queries    []query
 	}{
-		data: []struct {
-			lset   map[string]string
-			chunks [][]sample
-		}{
+		data: []seriesSamples{
 			{
 				lset: map[string]string{
 					"a": "a",