diff --git a/cmd/thanos/compact.go b/cmd/thanos/compact.go
index a789b70842b..e0bcc21755a 100644
--- a/cmd/thanos/compact.go
+++ b/cmd/thanos/compact.go
@@ -110,6 +110,10 @@ func registerCompact(m map[string]setupFunc, app *kingpin.Application, name stri
 	compactionConcurrency := cmd.Flag("compact.concurrency", "Number of goroutines to use when compacting groups.").
 		Default("1").Int()
 
+	includeShards := cmd.Flag("shard.include", "Prometheus shard to compact. May be specified multiple times. Cannot be used with --shards.exclude.").Strings()
+
+	excludeShards := cmd.Flag("shard.exclude", "Prometheus shard to ignore. May be specified multiple times. Cannot be used with --shards.include.").Strings()
+
 	m[name] = func(g *run.Group, logger log.Logger, reg *prometheus.Registry, tracer opentracing.Tracer, _ bool) error {
 		return runCompact(g, logger, reg,
 			*httpAddr,
@@ -130,6 +134,8 @@ func registerCompact(m map[string]setupFunc, app *kingpin.Application, name stri
 			*maxCompactionLevel,
 			*blockSyncConcurrency,
 			*compactionConcurrency,
+			*includeShards,
+			*excludeShards,
 		)
 	}
 }
@@ -152,6 +158,8 @@ func runCompact(
 	maxCompactionLevel int,
 	blockSyncConcurrency int,
 	concurrency int,
+	includeShards []string,
+	excludeShards []string,
 ) error {
 	halted := prometheus.NewGauge(prometheus.GaugeOpts{
 		Name: "thanos_compactor_halted",
@@ -166,6 +174,10 @@ func runCompact(
 	reg.MustRegister(halted)
 	reg.MustRegister(retried)
 
+	if len(includeShards) > 0 && len(excludeShards) > 0 {
+		return errors.New("Only one of --shard.include and --shard.exclude should be specified")
+	}
+
 	confContentYaml, err := objStoreConfig.Content()
 	if err != nil {
 		return err
@@ -184,7 +196,7 @@ func runCompact(
 	}()
 
 	sy, err := compact.NewSyncer(logger, reg, bkt, consistencyDelay,
-		blockSyncConcurrency, acceptMalformedIndex)
+		blockSyncConcurrency, acceptMalformedIndex, includeShards, excludeShards)
 	if err != nil {
 		return errors.Wrap(err, "create syncer")
 	}
diff --git a/pkg/compact/compact.go b/pkg/compact/compact.go
index 61a9f0be1dc..0803f3a9659 100644
--- a/pkg/compact/compact.go
+++ b/pkg/compact/compact.go
@@ -50,6 +50,8 @@ type Syncer struct {
 	blockSyncConcurrency int
 	metrics              *syncerMetrics
 	acceptMalformedIndex bool
+	includeShards        []string
+	excludeShards        []string
 }
 
 type syncerMetrics struct {
@@ -134,7 +136,8 @@ func newSyncerMetrics(reg prometheus.Registerer) *syncerMetrics {
 
 // NewSyncer returns a new Syncer for the given Bucket and directory.
 // Blocks must be at least as old as the sync delay for being considered.
-func NewSyncer(logger log.Logger, reg prometheus.Registerer, bkt objstore.Bucket, consistencyDelay time.Duration, blockSyncConcurrency int, acceptMalformedIndex bool) (*Syncer, error) {
+func NewSyncer(logger log.Logger, reg prometheus.Registerer, bkt objstore.Bucket, consistencyDelay time.Duration,
+	blockSyncConcurrency int, acceptMalformedIndex bool, includeShards []string, excludeShards []string) (*Syncer, error) {
 	if logger == nil {
 		logger = log.NewNopLogger()
 	}
@@ -147,6 +150,8 @@ func NewSyncer(logger log.Logger, reg prometheus.Registerer, bkt objstore.Bucket
 		metrics:              newSyncerMetrics(reg),
 		blockSyncConcurrency: blockSyncConcurrency,
 		acceptMalformedIndex: acceptMalformedIndex,
+		includeShards:        includeShards,
+		excludeShards:        excludeShards,
 	}, nil
 }
 
@@ -204,6 +209,13 @@ func (c *Syncer) syncMetas(ctx context.Context) error {
 					return
 				}
 
+				if shardLabel, ok := meta.Thanos.Labels["prometheus_shard"]; ok {
+					if c.shouldSkipShard(shardLabel) {
+						level.Debug(c.logger).Log("msg", "skipping shard", "label", shardLabel)
+						continue
+					}
+				}
+
 				c.blocksMtx.Lock()
 				c.blocks[id] = meta
 				c.blocksMtx.Unlock()
@@ -308,6 +320,32 @@ func (c *Syncer) removeIfMetaMalformed(ctx context.Context, id ulid.ULID) (remov
 	return true
 }
 
+func (c *Syncer) shouldSkipShard(shardLabel string) bool {
+
+	// If specified, shard must be present
+	if len(c.includeShards) > 0 {
+		for _, shard := range c.includeShards {
+			if shardLabel == shard {
+				return false
+			}
+		}
+		return true
+	}
+
+	// If specified, shard must *not* be present
+	if len(c.excludeShards) > 0 {
+		for _, shard := range c.excludeShards {
+			if shardLabel == shard {
+				return true
+			}
+		}
+		return false
+	}
+
+	// No shards specified, default is to include all.
+	return false
+}
+
 // GroupKey returns a unique identifier for the group the block belongs to. It considers
 // the downsampling resolution and the block's labels.
 func GroupKey(meta metadata.Meta) string {
diff --git a/pkg/compact/compact_e2e_test.go b/pkg/compact/compact_e2e_test.go
index f58862c0ac0..0618785d6f5 100644
--- a/pkg/compact/compact_e2e_test.go
+++ b/pkg/compact/compact_e2e_test.go
@@ -32,7 +32,7 @@ func TestSyncer_SyncMetas_e2e(t *testing.T) {
 		ctx, cancel := context.WithTimeout(context.Background(), 120*time.Second)
 		defer cancel()
 
-		sy, err := NewSyncer(nil, nil, bkt, 0, 1, false)
+		sy, err := NewSyncer(nil, nil, bkt, 0, 1, false, []string{}, []string{})
 		testutil.Ok(t, err)
 
 		// Generate 15 blocks. Initially the first 10 are synced into memory and only the last
@@ -134,7 +134,7 @@ func TestSyncer_GarbageCollect_e2e(t *testing.T) {
 		}
 
 		// Do one initial synchronization with the bucket.
-		sy, err := NewSyncer(nil, nil, bkt, 0, 1, false)
+		sy, err := NewSyncer(nil, nil, bkt, 0, 1, false, []string{}, []string{})
 		testutil.Ok(t, err)
 		testutil.Ok(t, sy.SyncMetas(ctx))
 
diff --git a/pkg/compact/compact_test.go b/pkg/compact/compact_test.go
index 4639fff67af..b0ad8674c8b 100644
--- a/pkg/compact/compact_test.go
+++ b/pkg/compact/compact_test.go
@@ -75,7 +75,7 @@ func TestSyncer_SyncMetas_HandlesMalformedBlocks(t *testing.T) {
 	defer cancel()
 
 	bkt := inmem.NewBucket()
-	sy, err := NewSyncer(nil, nil, bkt, 10*time.Second, 1, false)
+	sy, err := NewSyncer(nil, nil, bkt, 10*time.Second, 1, false, []string{}, []string{})
 	testutil.Ok(t, err)
 
 	// Generate 1 block which is older than MinimumAgeForRemoval which has chunk data but no meta.  Compactor should delete it.
@@ -103,3 +103,25 @@ func TestSyncer_SyncMetas_HandlesMalformedBlocks(t *testing.T) {
 	testutil.Ok(t, err)
 	testutil.Equals(t, true, exists)
 }
+
+func TestSyncer_ShouldSkipShard_SkipCorrectly(t *testing.T) {
+
+	sy, err := NewSyncer(nil, nil, nil, time.Second, 1, false, []string{}, []string{})
+	testutil.Ok(t, err)
+
+	testutil.Equals(t, false, sy.shouldSkipShard("prom-1"))
+
+	include := []string{"prom-2"}
+	sy, err = NewSyncer(nil, nil, nil, time.Second, 1, false, include, []string{})
+	testutil.Ok(t, err)
+
+	testutil.Equals(t, true, sy.shouldSkipShard("prom-1"))
+	testutil.Equals(t, false, sy.shouldSkipShard("prom-2"))
+
+	exclude := []string{"prom-3"}
+	sy, err = NewSyncer(nil, nil, nil, time.Second, 1, false, []string{}, exclude)
+	testutil.Ok(t, err)
+
+	testutil.Equals(t, true, sy.shouldSkipShard("prom-3"))
+	testutil.Equals(t, false, sy.shouldSkipShard("prom-1"))
+}