diff --git a/pkg/commands/run.go b/pkg/commands/run.go
index c255e24642a4..f5421e702eee 100644
--- a/pkg/commands/run.go
+++ b/pkg/commands/run.go
@@ -313,8 +313,15 @@ func fixSlicesFlags(fs *pflag.FlagSet) {
 			return
 		}
 
+		var safe []string
+		for _, v := range s {
+			// add quotes to escape comma because spf13/pflag use a CSV parser:
+			// https://github.com/spf13/pflag/blob/85dd5c8bc61cfa382fecd072378089d4e856579d/string_slice.go#L43
+			safe = append(safe, `"`+v+`"`)
+		}
+
 		// calling Set sets Changed to true: next Set calls will append, not overwrite
-		_ = f.Value.Set(strings.Join(s, ","))
+		_ = f.Value.Set(strings.Join(safe, ","))
 	})
 }
 
diff --git a/pkg/config/reader.go b/pkg/config/reader.go
index 00722ba6366d..6e97277daa2a 100644
--- a/pkg/config/reader.go
+++ b/pkg/config/reader.go
@@ -7,7 +7,7 @@ import (
 	"path/filepath"
 	"strings"
 
-	homedir "github.com/mitchellh/go-homedir"
+	"github.com/mitchellh/go-homedir"
 	"github.com/spf13/viper"
 
 	"github.com/golangci/golangci-lint/pkg/fsutils"
diff --git a/pkg/lint/runner.go b/pkg/lint/runner.go
index 26611c05ae63..c492f558020f 100644
--- a/pkg/lint/runner.go
+++ b/pkg/lint/runner.go
@@ -237,9 +237,9 @@ func (r *Runner) processIssues(issues []result.Issue, sw *timeutils.Stopwatch, s
 
 func getExcludeProcessor(cfg *config.Issues) processors.Processor {
 	var excludeTotalPattern string
-	excludeGlobalPatterns := cfg.ExcludePatterns
-	if len(excludeGlobalPatterns) != 0 {
-		excludeTotalPattern = fmt.Sprintf("(%s)", strings.Join(excludeGlobalPatterns, "|"))
+
+	if len(cfg.ExcludePatterns) != 0 {
+		excludeTotalPattern = fmt.Sprintf("(%s)", strings.Join(cfg.ExcludePatterns, "|"))
 	}
 
 	var excludeProcessor processors.Processor