diff --git a/lib/api/notes.rb b/lib/api/notes.rb
index 3efdfe2d46e..174473f5371 100644
--- a/lib/api/notes.rb
+++ b/lib/api/notes.rb
@@ -20,7 +20,19 @@ module API
         #   GET /projects/:id/snippets/:noteable_id/notes
         get ":id/#{noteables_str}/:#{noteable_id_str}/notes" do
           @noteable = user_project.send(:"#{noteables_str}").find(params[:"#{noteable_id_str}"])
-          present paginate(@noteable.notes), with: Entities::Note
+
+          # We exclude notes that are cross-references and that cannot be viewed
+          # by the current user. By doing this exclusion at this level and not
+          # at the DB query level (which we cannot in that case), the current
+          # page can have less elements than :per_page even if
+          # there's more than one page.
+          notes =
+            # paginate() only works with a relation. This could lead to a
+            # mismatch between the pagination headers info and the actual notes
+            # array returned, but this is really a edge-case.
+            paginate(@noteable.notes).
+            reject { |n| n.cross_reference_not_visible_for?(current_user) }
+          present notes, with: Entities::Note
         end
 
         # Get a single +noteable+ note
@@ -35,7 +47,12 @@ module API
         get ":id/#{noteables_str}/:#{noteable_id_str}/notes/:note_id" do
           @noteable = user_project.send(:"#{noteables_str}").find(params[:"#{noteable_id_str}"])
           @note = @noteable.notes.find(params[:note_id])
-          present @note, with: Entities::Note
+
+          if @note.cross_reference_not_visible_for?(current_user)
+            not_found!("Note")
+          else
+            present @note, with: Entities::Note
+          end
         end
 
         # Create a new +noteable+ note
diff --git a/spec/requests/api/notes_spec.rb b/spec/requests/api/notes_spec.rb
index 8b177af4689..565805d870c 100644
--- a/spec/requests/api/notes_spec.rb
+++ b/spec/requests/api/notes_spec.rb
@@ -10,6 +10,24 @@ describe API::API, api: true  do
   let!(:issue_note) { create(:note, noteable: issue, project: project, author: user) }
   let!(:merge_request_note) { create(:note, noteable: merge_request, project: project, author: user) }
   let!(:snippet_note) { create(:note, noteable: snippet, project: project, author: user) }
+
+  # For testing the cross-reference of a private issue in a public issue
+  let(:private_user)    { create(:user) }
+  let(:private_project) {
+    create(:project, namespace: private_user.namespace).
+    tap { |p| p.team << [private_user, :master] }
+  }
+  let(:private_issue)   { create(:issue, project: private_project) }
+  let(:ext_proj)  { create(:project, :public) }
+  let(:ext_issue) { create(:issue, project: ext_proj) }
+
+  let!(:cross_reference_note) {
+    create :note,
+    noteable: ext_issue, project: ext_proj,
+    note: "mentioned in issue #{private_issue.to_reference(ext_proj)}",
+    system: true
+  }
+
   before { project.team << [user, :reporter] }
 
   describe "GET /projects/:id/noteable/:noteable_id/notes" do
@@ -25,6 +43,24 @@ describe API::API, api: true  do
         get api("/projects/#{project.id}/issues/123/notes", user)
         expect(response.status).to eq(404)
       end
+
+      context "that references a private issue" do
+        it "should return an empty array" do
+          get api("/projects/#{ext_proj.id}/issues/#{ext_issue.id}/notes", user)
+          expect(response.status).to eq(200)
+          expect(json_response).to be_an Array
+          expect(json_response).to be_empty
+        end
+
+        context "and current user can view the note" do
+          it "should return an empty array" do
+            get api("/projects/#{ext_proj.id}/issues/#{ext_issue.id}/notes", private_user)
+            expect(response.status).to eq(200)
+            expect(json_response).to be_an Array
+            expect(json_response.first['body']).to eq(cross_reference_note.note)
+          end
+        end
+      end
     end
 
     context "when noteable is a Snippet" do
@@ -68,6 +104,21 @@ describe API::API, api: true  do
         get api("/projects/#{project.id}/issues/#{issue.id}/notes/123", user)
         expect(response.status).to eq(404)
       end
+
+      context "that references a private issue" do
+        it "should return a 404 error" do
+          get api("/projects/#{ext_proj.id}/issues/#{ext_issue.id}/notes/#{cross_reference_note.id}", user)
+          expect(response.status).to eq(404)
+        end
+
+        context "and current user can view the note" do
+          it "should return an issue note by id" do
+            get api("/projects/#{ext_proj.id}/issues/#{ext_issue.id}/notes/#{cross_reference_note.id}", private_user)
+            expect(response.status).to eq(200)
+            expect(json_response['body']).to eq(cross_reference_note.note)
+          end
+        end
+      end
     end
 
     context "when noteable is a Snippet" do