diff --git a/lisp/gnus/gnus-search.el b/lisp/gnus/gnus-search.el
index d64c0cb90c..bb7fd47eb6 100644
--- a/lisp/gnus/gnus-search.el
+++ b/lisp/gnus/gnus-search.el
@@ -1606,13 +1606,17 @@ gnus-search-run-search
 			    proc-buffer program cp-list))
 	  (while (process-live-p proc)
 	    (accept-process-output proc))
-	  (while (re-search-forward "^thread:\\([^ ]+\\)" (point-max) t)
-	    (push (match-string 1) thread-ids))
+          (goto-char (point-min))
+	  (while (re-search-forward "^thread:\\([^[:space:]\n]+\\)" (point-max) t)
+	    (cl-pushnew (match-string 1) thread-ids :test #'equal))
 	  (cl-call-next-method
 	   engine server
-	   ;; Completely replace the query with our new thread-based one.
-	   (mapconcat (lambda (thrd) (concat "thread:" thrd))
-		      thread-ids " or ")
+	   ;; If we found threads, completely replace the query with
+	   ;; our new thread-based one.
+           (if thread-ids
+	       (mapconcat (lambda (thrd) (concat "thread:" thrd))
+		          thread-ids " or ")
+             query)
 	   nil)))
     (cl-call-next-method engine server query groups)))
 
@@ -1629,8 +1633,9 @@ gnus-search-indexed-search-command
 	"search"
 	,(if thread
 	     "--output=threads"
-	   "--output=files")
-	"--duplicate=1" ; I have found this necessary, I don't know why.
+           ;; No one knows why this "duplicate" flag is necessary, but
+           ;; it doesn't work with a thread search.
+	   "--output=files --duplicate=1")
 	,@switches
 	,(if limit (format "--limit=%d" limit) "")
 	,qstring