diff --git a/.bazelrc b/.bazelrc
index 2d2ed2b..e83c5da 100644
--- a/.bazelrc
+++ b/.bazelrc
@@ -1,2 +1,4 @@
 build:clang-tidy --aspects @bazel_clang_tidy//clang_tidy:clang_tidy.bzl%clang_tidy_aspect
-build:clang-tidy --output_groups=report
\ No newline at end of file
+build:clang-tidy --output_groups=report
+build:clang-tidy --@bazel_clang_tidy//:clang_tidy_bazel_out_includes_are_system_includes=True
+build:clang-tidy --@bazel_clang_tidy//:clang_tidy_virtual_includes_are_system_includes=True
diff --git a/BUILD b/BUILD
index eaec502..6be41aa 100644
--- a/BUILD
+++ b/BUILD
@@ -1,3 +1,5 @@
+load("@bazel_skylib//rules:common_settings.bzl", "bool_flag")
+
 filegroup(
     name = "clang_tidy_config_default",
     srcs = [
@@ -33,3 +35,15 @@ label_flag(
     build_setting_default = ":clang_tidy_additional_deps_default",
     visibility = ["//visibility:public"],
 )
+
+bool_flag(
+    name = "clang_tidy_bazel_out_includes_are_system_includes",
+    build_setting_default = False,
+    visibility = ["//visibility:public"],
+)
+
+bool_flag(
+    name = "clang_tidy_virtual_includes_are_system_includes",
+    build_setting_default = False,
+    visibility = ["//visibility:public"],
+)
diff --git a/WORKSPACE b/WORKSPACE
index adfd402..ec2d035 100644
--- a/WORKSPACE
+++ b/WORKSPACE
@@ -1 +1,15 @@
 workspace(name = "bazel_clang_tidy")
+
+load("@bazel_tools//tools/build_defs/repo:utils.bzl", "maybe")
+load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")
+
+maybe(
+    http_archive,
+    name = "bazel_skylib",
+    sha256 = "cd55a062e763b9349921f0f5db8c3933288dc8ba4f76dd9416aac68acee3cb94",
+    url = "https://github.com/bazelbuild/bazel-skylib/releases/download/1.5.0/bazel-skylib-1.5.0.tar.gz",
+)
+
+load("@bazel_skylib//:workspace.bzl", "bazel_skylib_workspace")
+
+bazel_skylib_workspace()
diff --git a/clang_tidy/clang_tidy.bzl b/clang_tidy/clang_tidy.bzl
index 4d515fc..a6bf7ef 100644
--- a/clang_tidy/clang_tidy.bzl
+++ b/clang_tidy/clang_tidy.bzl
@@ -59,12 +59,33 @@ def _run_tidy(
     for i in compilation_context.framework_includes.to_list():
         args.add("-F" + i)
 
-    for i in compilation_context.includes.to_list():
-        args.add("-I" + i)
-
-    args.add_all(compilation_context.quote_includes.to_list(), before_each = "-iquote")
+    isystems = compilation_context.system_includes.to_list()
+
+    if ctx.attr._clang_tidy_virtual_includes_are_system_includes:
+        # Include anything that uses include_prefix or strip_include_prefix as a system include
+        include_dirs = []
+        for include in compilation_context.includes.to_list():
+            if "/_virtual_includes/" in include:
+                isystems.append(include)
+            else:
+                include_dirs.append(include)
+    else:
+        include_dirs = compilation_context.includes.to_list()
+
+    if ctx.attr._clang_tidy_bazel_out_includes_are_system_includes:
+        # Treat generated code in bazel-out/ as system include
+        iquotes = []
+        for quote_include in compilation_context.quote_includes.to_list():
+            if quote_include.startswith("bazel-out/"):
+                isystems.append(quote_include)
+            else:
+                iquotes.append(quote_include)
+    else:
+        iquotes = compilation_context.quote_includes.to_list()
 
-    args.add_all(compilation_context.system_includes.to_list(), before_each = "-isystem")
+    args.add_all(include_dirs, before_each = "-I")
+    args.add_all(iquotes, before_each = "-iquote")
+    args.add_all(isystems, before_each = "-isystem")
 
     ctx.actions.run(
         inputs = inputs,
@@ -184,6 +205,8 @@ clang_tidy_aspect = aspect(
         "_clang_tidy_executable": attr.label(default = Label("//:clang_tidy_executable")),
         "_clang_tidy_additional_deps": attr.label(default = Label("//:clang_tidy_additional_deps")),
         "_clang_tidy_config": attr.label(default = Label("//:clang_tidy_config")),
+        "_clang_tidy_bazel_out_includes_are_system_includes": attr.label(default = Label("//:clang_tidy_bazel_out_includes_are_system_includes")),
+        "_clang_tidy_virtual_includes_are_system_includes": attr.label(default = Label("//:clang_tidy_virtual_includes_are_system_includes")),
     },
     toolchains = ["@bazel_tools//tools/cpp:toolchain_type"],
 )