diff --git a/pkg/lint/service.go b/pkg/lint/service.go
index 9b3e09e..4734fd6 100644
--- a/pkg/lint/service.go
+++ b/pkg/lint/service.go
@@ -420,6 +420,9 @@ func collectConfiguredFiles(projectPath string, paths []string, excludes []strin
 
 		addFile := func(candidate string) {
 			relativePath := relativeConfiguredPath(projectPath, candidate)
+			if hasHiddenDirectory(relativePath) || hasHiddenDirectory(filepath.ToSlash(filepath.Clean(candidate))) {
+				return
+			}
 			if matchesConfiguredExclude(relativePath, excludes) || matchesConfiguredExclude(filepath.ToSlash(filepath.Clean(candidate)), excludes) {
 				return
 			}
@@ -493,6 +496,22 @@ func matchesConfiguredExclude(candidate string, excludes []string) bool {
 	return false
 }
 
+func hasHiddenDirectory(candidate string) bool {
+	if candidate == "" {
+		return false
+	}
+
+	for _, segment := range strings.Split(filepath.ToSlash(filepath.Clean(candidate)), "/") {
+		if segment == "" || segment == "." || segment == ".." {
+			continue
+		}
+		if strings.HasPrefix(segment, ".") {
+			return true
+		}
+	}
+	return false
+}
+
 func enabledToolNames(config LintConfig, languages []string, input RunInput, categories []string) []string {
 	var names []string
 
diff --git a/pkg/lint/service_test.go b/pkg/lint/service_test.go
index 0d50bc2..fe8ea91 100644
--- a/pkg/lint/service_test.go
+++ b/pkg/lint/service_test.go
@@ -189,6 +189,48 @@ func Run() {
 	assert.True(t, report.Summary.Passed)
 }
 
+func TestServiceRun_Good_SkipsHiddenConfiguredFilePath(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "go.mod"), []byte("module example.com/test\n"), 0o644))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "root.go"), []byte(`package sample
+
+type service struct{}
+
+func (service) Process(string) error { return nil }
+
+func Run() {
+	svc := service{}
+	_ = svc.Process("root")
+}
+`), 0o644))
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, ".hidden"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, ".hidden", "scoped.go"), []byte(`package sample
+
+type service struct{}
+
+func (service) Process(string) error { return nil }
+
+func Run() {
+	svc := service{}
+	_ = svc.Process("hidden")
+}
+`), 0o644))
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, ".core"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, ".core", "lint.yaml"), []byte("paths:\n  - root.go\n  - .hidden/scoped.go\n"), 0o644))
+
+	svc := &Service{adapters: []Adapter{newCatalogAdapter()}}
+	report, err := svc.Run(context.Background(), RunInput{
+		Path:   dir,
+		FailOn: "warning",
+	})
+	require.NoError(t, err)
+
+	require.Len(t, report.Findings, 1)
+	assert.Equal(t, "root.go", report.Findings[0].File)
+	assert.Equal(t, 1, report.Summary.Total)
+	assert.False(t, report.Summary.Passed)
+}
+
 func TestServiceRun_Good_UsesNamedSchedule(t *testing.T) {
 	dir := t.TempDir()
 	require.NoError(t, os.WriteFile(filepath.Join(dir, "go.mod"), []byte("module example.com/test\n"), 0o644))