diff --git a/gtk2_ardour/rhythm_ferret.cc b/gtk2_ardour/rhythm_ferret.cc
index da31feca3c..5685cb56af 100644
--- a/gtk2_ardour/rhythm_ferret.cc
+++ b/gtk2_ardour/rhythm_ferret.cc
@@ -183,15 +183,17 @@ RhythmFerret::run_analysis ()
 		return;
 	}
 
-	RegionSelection& regions (editor.get_selection().regions);
+	clear_transients ();
+
+	regions_with_transients = editor.get_selection().regions;
 
 	current_results.clear ();
 
-	if (regions.empty()) {
+	if (regions_with_transients.empty()) {
 		return;
 	}
 
-	for (RegionSelection::iterator i = regions.begin(); i != regions.end(); ++i) {
+	for (RegionSelection::iterator i = regions_with_transients.begin(); i != regions_with_transients.end(); ++i) {
 
 		boost::shared_ptr<Readable> rd = boost::static_pointer_cast<AudioRegion> ((*i)->region());
 
@@ -382,5 +384,17 @@ void
 RhythmFerret::on_hide ()
 {
 	ArdourDialog::on_hide ();
+	clear_transients ();
+}
+
+/* Clear any transients that we have added */
+void
+RhythmFerret::clear_transients ()
+{
+	current_results.clear ();
+	for (RegionSelection::iterator i = regions_with_transients.begin(); i != regions_with_transients.end(); ++i) {
+		(*i)->region()->set_transients (current_results);
+	}
+	regions_with_transients.clear ();
 }
 
diff --git a/gtk2_ardour/rhythm_ferret.h b/gtk2_ardour/rhythm_ferret.h
index 1d84645056..a1a201531b 100644
--- a/gtk2_ardour/rhythm_ferret.h
+++ b/gtk2_ardour/rhythm_ferret.h
@@ -12,6 +12,7 @@
 #include <gtkmm/button.h>
 
 #include "ardour_dialog.h"
+#include "region_selection.h"
 
 namespace ARDOUR {
 	class Readable;
@@ -79,6 +80,10 @@ class RhythmFerret : public ArdourDialog {
 
 	ARDOUR::AnalysisFeatureList current_results;
 
+	void clear_transients ();
+	/** Regions that we have added transient marks to */
+	RegionSelection regions_with_transients;
+
 	AnalysisMode get_analysis_mode () const;
 	Action get_action() const;
 	void analysis_mode_changed ();