diff --git a/jackdriver.c b/jackdriver.c
index aef4d87..f29ed31 100644
--- a/jackdriver.c
+++ b/jackdriver.c
@@ -151,7 +151,7 @@ process_midi_input(JACK_SEQ* seq,jack_nframes_t nframes)
 
     void *port_buffer = jack_port_get_buffer(seq->input_port[k], nframes);
     // this is used for direct pass-through of system messages
-    void *out_buffer = seq->passthrough && k < seq->n_out?
+    void *out_buffer = seq->passthrough[k] && k < seq->n_out?
       jack_port_get_buffer(seq->output_port[k], nframes):0;
     if (port_buffer == NULL)
     {
@@ -233,7 +233,7 @@ process_midi_output(JACK_SEQ* seq,jack_nframes_t nframes)
       return;
     }
 
-    if (!seq->passthrough)
+    if (!seq->passthrough[k])
     {
 #ifdef JACK_MIDI_NEEDS_NFRAMES
       jack_midi_clear_buffer(port_buffer, nframes);
diff --git a/jackdriver.h b/jackdriver.h
index 4a94c86..72cee35 100644
--- a/jackdriver.h
+++ b/jackdriver.h
@@ -11,7 +11,7 @@ typedef struct _jseq
   jack_client_t	*jack_client;
   jack_port_t	**output_port;
   jack_port_t	**input_port;
-  uint8_t n_in, n_out, passthrough;
+  uint8_t n_in, n_out, passthrough[2];
 } JACK_SEQ;
 
 extern int jack_quit;
diff --git a/midizap.c b/midizap.c
index 88b26ef..b4405a7 100644
--- a/midizap.c
+++ b/midizap.c
@@ -21,7 +21,7 @@ Display *display;
 
 JACK_SEQ seq;
 int jack_num_outputs = 0, debug_jack = 0;
-int auto_feedback = 1, system_passthrough = 0;
+int auto_feedback = 1, system_passthrough[2] = {-1, -1};
 int shift = 0;
 
 void
@@ -1579,7 +1579,7 @@ handle_event(uint8_t *msg, uint8_t portno, int depth, int recursive)
 
 void help(char *progname)
 {
-  fprintf(stderr, "Usage: %s [-hkns] [-d[rskmj]] [-o[n]] [-j name] [-P[prio]] [-r rcfile]\n", progname);
+  fprintf(stderr, "Usage: %s [-hkn] [-d[rskmj]] [-os[n]] [-j name] [-P[prio]] [-r rcfile]\n", progname);
   fprintf(stderr, "-h print this message\n");
   fprintf(stderr, "-d debug (r = regex, s = strokes, k = keys, m = midi, j = jack; default: all)\n");
   fprintf(stderr, "-j jack client name (default: midizap)\n");
@@ -1588,7 +1588,7 @@ void help(char *progname)
   fprintf(stderr, "-o set number of MIDI output ports (0-2, default: 1)\n");
   fprintf(stderr, "-P set real-time priority (default: 90)\n");
   fprintf(stderr, "-r config file name (default: MIDIZAP_CONFIG_FILE variable or ~/.midizaprc)\n");
-  fprintf(stderr, "-s pass-through of system messages\n");
+  fprintf(stderr, "-s pass-through of system messages (0-2; default: all ports)\n");
 }
 
 uint8_t quit = 0;
@@ -1665,7 +1665,7 @@ main(int argc, char **argv)
   // Start recording the command line to be passed to Jack session management.
   add_command(argv[0], 0);
 
-  while ((opt = getopt(argc, argv, "hkno::d::j:r:P::s")) != -1) {
+  while ((opt = getopt(argc, argv, "hkno::d::j:r:P::s::")) != -1) {
     switch (opt) {
     case 'h':
       help(argv[0]);
@@ -1758,8 +1758,28 @@ main(int argc, char **argv)
       }
       break;
     case 's':
-      system_passthrough = 1;
-      add_command("-s", 1);
+      if (optarg && *optarg) {
+	const char *a = optarg;
+	if (!strcmp(a, "2")) {
+	  system_passthrough[0] = 0;
+	  system_passthrough[1] = 1;
+	  add_command("-s2", 1);
+	} else if (!strcmp(a, "1")) {
+	  system_passthrough[0] = 1;
+	  system_passthrough[1] = 0;
+	  add_command("-s1", 1);
+	} else if (!strcmp(a, "0")) {
+	  system_passthrough[0] = system_passthrough[1] = 0;
+	  add_command("-s0", 1);
+	} else {
+	  fprintf(stderr, "%s: wrong port number (-s), must be 0, 1 or 2\n", argv[0]);
+	  fprintf(stderr, "Try -h for help.\n");
+	  exit(1);
+	}
+      } else {
+	system_passthrough[0] = system_passthrough[1] = 1;
+	add_command("-s", 1);
+      }
       break;
     default:
       fprintf(stderr, "Try -h for help.\n");
@@ -1786,7 +1806,8 @@ main(int argc, char **argv)
   seq.client_name = jack_client_name;
   seq.n_in = jack_num_outputs>1?jack_num_outputs:1;
   seq.n_out = jack_num_outputs>0?jack_num_outputs:0;
-  seq.passthrough = jack_num_outputs>0?system_passthrough:0;
+  seq.passthrough[0] = jack_num_outputs>0?system_passthrough[0]>0:0;
+  seq.passthrough[1] = jack_num_outputs>1?system_passthrough[1]>0:0;
   if (!init_jack(&seq, debug_jack)) {
     exit(1);
   }
diff --git a/midizap.h b/midizap.h
index e39895e..b4a88e7 100644
--- a/midizap.h
+++ b/midizap.h
@@ -134,6 +134,6 @@ extern int debug_regex, debug_strokes, debug_keys, debug_midi;
 extern int default_debug_regex, default_debug_strokes, default_debug_keys,
   default_debug_midi;
 extern char *config_file_name;
-extern int jack_num_outputs, system_passthrough, auto_feedback;
+extern int jack_num_outputs, system_passthrough[2], auto_feedback;
 extern int midi_octave, shift;
 extern char *jack_client_name;
diff --git a/readconfig.c b/readconfig.c
index 33fb913..862749b 100644
--- a/readconfig.c
+++ b/readconfig.c
@@ -1914,10 +1914,6 @@ read_config_file(void)
 	auto_feedback = 0; // -n
 	continue;
       }
-      if (!strcmp(tok, "SYSTEM_PASSTHROUGH")) {
-	system_passthrough = 1; // -s
-	continue;
-      }
       if (!strcmp(tok, "JACK_NAME")) {
 	char *a = token(NULL, &delim);
 	if (!jack_client_name) {
@@ -1939,6 +1935,22 @@ read_config_file(void)
 	}
 	continue;
       }
+      if (!strcmp(tok, "SYSTEM_PASSTHROUGH")) { // -s
+	char *a = token(NULL, &delim);
+	int k, n;
+	if (a && *a && *a != '#') {
+	  if (sscanf(a, "%d%n", &k, &n) == 1 && !a[n] && k>=0 && k<=2) {
+	    if (system_passthrough[0] < 0) system_passthrough[0] = k==1;
+	    if (system_passthrough[1] < 0) system_passthrough[1] = k==2;
+	  } else {
+	    fprintf(stderr, "invalid port number: %s, must be 0, 1 or 2\n", a);
+	  }
+	} else {
+	  if (system_passthrough[0] < 0) system_passthrough[0] = 1;
+	  if (system_passthrough[1] < 0) system_passthrough[1] = 1;
+	}
+	continue;
+      }
       if (!strncmp(tok, "MIDI_OCTAVE", 11)) {
 	char *a = tok+11;
 	int k, n;