diff --git a/git-send-email.perl b/git-send-email.perl
index 1f425c0809..29910576d7 100755
--- a/git-send-email.perl
+++ b/git-send-email.perl
@@ -1608,7 +1608,6 @@ sub send_message {
 
 $in_reply_to = $initial_in_reply_to;
 $references = $initial_in_reply_to || '';
-$subject = $initial_subject;
 $message_num = 0;
 
 # Prepares the email, prompts the user, sends it out
@@ -1631,6 +1630,7 @@ sub process_file {
 	@xh = ();
 	my $input_format = undef;
 	my @header = ();
+	$subject = $initial_subject;
 	$message = "";
 	$message_num++;
 	# First unfold multiline header fields
@@ -1837,15 +1837,23 @@ sub process_file {
 	}
 
 	# set up for the next message
-	if ($thread && $message_was_sent &&
-		($chain_reply_to || !defined $in_reply_to || length($in_reply_to) == 0 ||
-		$message_num == 1)) {
-		$in_reply_to = $message_id;
-		if (length $references > 0) {
-			$references .= "\n $message_id";
-		} else {
-			$references = "$message_id";
+	if ($thread) {
+		if ($message_was_sent &&
+		  ($chain_reply_to || !defined $in_reply_to || length($in_reply_to) == 0 ||
+		  $message_num == 1)) {
+			$in_reply_to = $message_id;
+			if (length $references > 0) {
+				$references .= "\n $message_id";
+			} else {
+				$references = "$message_id";
+			}
 		}
+	} elsif (!defined $initial_in_reply_to) {
+		# --thread and --in-reply-to manage the "In-Reply-To" header and by
+		# extension the "References" header. If these commands are not used, reset
+		# the header values to their defaults.
+		$in_reply_to = undef;
+		$references = '';
 	}
 	$message_id = undef;
 	$num_sent++;
diff --git a/t/t9001-send-email.sh b/t/t9001-send-email.sh
index 4eee9c3dcb..35be6b0190 100755
--- a/t/t9001-send-email.sh
+++ b/t/t9001-send-email.sh
@@ -2097,6 +2097,51 @@ test_expect_success $PREREQ 'leading and trailing whitespaces are removed' '
 	test_cmp expected-list actual-list
 '
 
+test_expect_success $PREREQ 'set up in-reply-to/references patches' '
+	cat >has-reply.patch <<-\EOF &&
+	From: A U Thor <author@example.com>
+	Subject: patch with in-reply-to
+	Message-ID: <patch.with.in.reply.to@example.com>
+	In-Reply-To: <replied.to@example.com>
+	References: <replied.to@example.com>
+
+	This is the body.
+	EOF
+	cat >no-reply.patch <<-\EOF
+	From: A U Thor <author@example.com>
+	Subject: patch without in-reply-to
+	Message-ID: <patch.without.in.reply.to@example.com>
+
+	This is the body.
+	EOF
+'
+
+test_expect_success $PREREQ 'patch reply headers correct with --no-thread' '
+	clean_fake_sendmail &&
+	git send-email \
+		--no-thread \
+		--to=nobody@example.com \
+		--smtp-server="$(pwd)/fake.sendmail" \
+		has-reply.patch no-reply.patch &&
+	grep "In-Reply-To: <replied.to@example.com>" msgtxt1 &&
+	grep "References: <replied.to@example.com>" msgtxt1 &&
+	! grep replied.to@example.com msgtxt2
+'
+
+test_expect_success $PREREQ 'cmdline in-reply-to used with --no-thread' '
+	clean_fake_sendmail &&
+	git send-email \
+		--no-thread \
+		--in-reply-to="<cmdline.reply@example.com>" \
+		--to=nobody@example.com \
+		--smtp-server="$(pwd)/fake.sendmail" \
+		has-reply.patch no-reply.patch &&
+	grep "In-Reply-To: <cmdline.reply@example.com>" msgtxt1 &&
+	grep "References: <cmdline.reply@example.com>" msgtxt1 &&
+	grep "In-Reply-To: <cmdline.reply@example.com>" msgtxt2 &&
+	grep "References: <cmdline.reply@example.com>" msgtxt2
+'
+
 test_expect_success $PREREQ 'invoke hook' '
 	mkdir -p .git/hooks &&