diff --git a/go/packages/golist.go b/go/packages/golist.go
index c4a1bd687f..54b0dbba50 100644
--- a/go/packages/golist.go
+++ b/go/packages/golist.go
@@ -130,12 +130,13 @@ extractQueries:
 		response.Packages = append(response.Packages, p)
 	}
 
+	var containsCandidates []string
+
 	if len(containFiles) != 0 {
-		containsResults, err := runContainsQueries(cfg, listfunc, isFallback, addPkg, containFiles)
+		containsCandidates, err = runContainsQueries(cfg, listfunc, isFallback, addPkg, containFiles)
 		if err != nil {
 			return nil, err
 		}
-		response.Roots = append(response.Roots, containsResults...)
 	}
 
 	if len(packagesNamed) != 0 {
@@ -146,12 +147,33 @@ extractQueries:
 		response.Roots = append(response.Roots, namedResults...)
 	}
 
-	needPkgs, err := processGolistOverlay(cfg, response)
+	modifiedPkgs, needPkgs, err := processGolistOverlay(cfg, response)
 	if err != nil {
 		return nil, err
 	}
+	if len(containFiles) > 0 {
+		containsCandidates = append(containsCandidates, modifiedPkgs...)
+		containsCandidates = append(containsCandidates, needPkgs...)
+	}
+
 	if len(needPkgs) > 0 {
 		addNeededOverlayPackages(cfg, listfunc, addPkg, needPkgs)
+		if err != nil {
+			return nil, err
+		}
+	}
+	// Check candidate packages for containFiles.
+	if len(containFiles) > 0 {
+		for _, id := range containsCandidates {
+			pkg := seenPkgs[id]
+			for _, f := range containFiles {
+				for _, g := range pkg.GoFiles {
+					if sameFile(f, g) {
+						response.Roots = append(response.Roots, id)
+					}
+				}
+			}
+		}
 	}
 
 	return response, nil
diff --git a/go/packages/golist_overlay.go b/go/packages/golist_overlay.go
index 60438a1acd..71ffcd9d55 100644
--- a/go/packages/golist_overlay.go
+++ b/go/packages/golist_overlay.go
@@ -16,9 +16,10 @@ import (
 // - adding test and non-test files to test variants of packages
 // - determining the correct package to add given a new import path
 // - creating packages that don't exist
-func processGolistOverlay(cfg *Config, response *driverResponse) (needPkgs []string, err error) {
+func processGolistOverlay(cfg *Config, response *driverResponse) (modifiedPkgs, needPkgs []string, err error) {
 	havePkgs := make(map[string]string) // importPath -> non-test package ID
 	needPkgsSet := make(map[string]bool)
+	modifiedPkgsSet := make(map[string]bool)
 
 	for _, pkg := range response.Packages {
 		// This is an approximation of import path to id. This can be
@@ -49,6 +50,7 @@ outer:
 				if !fileExists {
 					pkg.GoFiles = append(pkg.GoFiles, path) // TODO(matloob): should the file just be added to GoFiles?
 					pkg.CompiledGoFiles = append(pkg.CompiledGoFiles, path)
+					modifiedPkgsSet[pkg.ID] = true
 				}
 				imports, err := extractImports(path, contents)
 				if err != nil {
@@ -77,7 +79,11 @@ outer:
 	for pkg := range needPkgsSet {
 		needPkgs = append(needPkgs, pkg)
 	}
-	return needPkgs, err
+	modifiedPkgs = make([]string, 0, len(modifiedPkgsSet))
+	for pkg := range modifiedPkgsSet {
+		modifiedPkgs = append(modifiedPkgs, pkg)
+	}
+	return modifiedPkgs, needPkgs, err
 }
 
 func extractImports(filename string, contents []byte) ([]string, error) {
diff --git a/go/packages/packages_test.go b/go/packages/packages_test.go
index 207996919c..39095bf918 100644
--- a/go/packages/packages_test.go
+++ b/go/packages/packages_test.go
@@ -1058,6 +1058,35 @@ func testContains(t *testing.T, exporter packagestest.Exporter) {
 	}
 }
 
+func TestContainsOverlay(t *testing.T) { packagestest.TestAll(t, testContainsOverlay) }
+func testContainsOverlay(t *testing.T, exporter packagestest.Exporter) {
+	exported := packagestest.Export(t, exporter, []packagestest.Module{{
+		Name: "golang.org/fake",
+		Files: map[string]interface{}{
+			"a/a.go": `package a; import "golang.org/fake/b"`,
+			"b/b.go": `package b; import "golang.org/fake/c"`,
+			"c/c.go": `package c`,
+		}}})
+	defer exported.Cleanup()
+	bOverlayFile := filepath.Join(filepath.Dir(exported.File("golang.org/fake", "b/b.go")), "b_overlay.go")
+	exported.Config.Mode = packages.LoadImports
+	exported.Config.Overlay = map[string][]byte{bOverlayFile: []byte(`package b;`)}
+	initial, err := packages.Load(exported.Config, "file="+bOverlayFile)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	graph, _ := importGraph(initial)
+	wantGraph := `
+* golang.org/fake/b
+  golang.org/fake/c
+  golang.org/fake/b -> golang.org/fake/c
+`[1:]
+	if graph != wantGraph {
+		t.Errorf("wrong import graph: got <<%s>>, want <<%s>>", graph, wantGraph)
+	}
+}
+
 // This test ensures that the effective GOARCH variable in the
 // application determines the Sizes function used by the type checker.
 // This behavior is a stop-gap until we make the build system's query