diff --git a/test/notmuch-test b/test/notmuch-test
index 27a144ef..a0c47d49 100755
--- a/test/notmuch-test
+++ b/test/notmuch-test
@@ -65,6 +65,7 @@ TESTS="
   hex-escaping
   parse-time-string
   search-date
+  thread-replies
 "
 TESTS=${NOTMUCH_TESTS:=$TESTS}
 
diff --git a/test/thread-replies b/test/thread-replies
new file mode 100755
index 00000000..5fc5eedd
--- /dev/null
+++ b/test/thread-replies
@@ -0,0 +1,144 @@
+#!/usr/bin/env bash
+#
+# Copyright (c) 2013 Aaron Ecay
+#
+
+test_description='test of proper handling of in-reply-to and references headers'
+
+# This test makes sure that the thread structure in the notmuch
+# database is constructed properly, even in the presence of
+# non-RFC-compliant headers'
+
+. ./test-lib.sh
+
+test_begin_subtest "Use References when In-Reply-To is broken"
+test_subtest_known_broken
+add_message '[id]="foo@one.com"' \
+    '[subject]=one'
+add_message '[in-reply-to]="mumble"' \
+    '[references]="<foo@one.com>"' \
+    '[subject]="Re: one"'
+output=$(notmuch show --format=json 'subject:one' | notmuch_json_show_sanitize)
+expected='[[[{"id": "foo@one.com",
+ "match": true,
+ "excluded": false,
+ "filename": "YYYYY",
+ "timestamp": 978709437,
+ "date_relative": "2001-01-05",
+ "tags": ["inbox", "unread"],
+ "headers": {"Subject": "one",
+ "From": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "To": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "Date": "Fri, 05 Jan 2001 15:43:57 +0000"},
+ "body": [{"id": 1,
+ "content-type": "text/plain",
+ "content": "This is just a test message (#1)\n"}]},
+ [[{"id": "msg-002@notmuch-test-suite",
+ "match": true, "excluded": false,
+ "filename": "YYYYY",
+ "timestamp": 978709437, "date_relative": "2001-01-05",
+ "tags": ["inbox", "unread"], "headers": {"Subject": "Re: one",
+ "From": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "To": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "Date": "Fri, 05 Jan 2001 15:43:57 +0000"},
+ "body": [{"id": 1, "content-type": "text/plain",
+ "content": "This is just a test message (#2)\n"}]}, []]]]]]'
+expected=`echo "$expected" | notmuch_json_show_sanitize`
+test_expect_equal_json "$output" "$expected"
+
+test_begin_subtest "Prefer References to In-Reply-To"
+test_subtest_known_broken
+add_message '[id]="foo@two.com"' \
+    '[subject]=two'
+add_message '[in-reply-to]="<bar@baz.com>"' \
+    '[references]="<foo@two.com>"' \
+    '[subject]="Re: two"'
+output=$(notmuch show --format=json 'subject:two' | notmuch_json_show_sanitize)
+expected='[[[{"id": "foo@two.com",
+ "match": true, "excluded": false,
+ "filename": "YYYYY",
+ "timestamp": 978709437, "date_relative": "2001-01-05", "tags": ["inbox", "unread"],
+ "headers": {"Subject": "two",
+ "From": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "To": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "Date": "Fri, 05 Jan 2001 15:43:57 +0000"},
+ "body": [{"id": 1, "content-type": "text/plain",
+ "content": "This is just a test message (#3)\n"}]},
+ [[{"id": "msg-004@notmuch-test-suite", "match": true, "excluded": false,
+ "filename": "YYYYY",
+ "timestamp": 978709437, "date_relative": "2001-01-05", "tags": ["inbox", "unread"],
+ "headers": {"Subject": "Re: two",
+ "From": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "To": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "Date": "Fri, 05 Jan 2001 15:43:57 +0000"},
+ "body": [{"id": 1,
+ "content-type": "text/plain", "content": "This is just a test message (#4)\n"}]},
+ []]]]]]'
+expected=`echo "$expected" | notmuch_json_show_sanitize`
+test_expect_equal_json "$output" "$expected"
+
+test_begin_subtest "Use In-Reply-To when no References"
+add_message '[id]="foo@three.com"' \
+    '[subject]="three"'
+add_message '[in-reply-to]="<foo@three.com>"' \
+    '[subject]="Re: three"'
+output=$(notmuch show --format=json 'subject:three' | notmuch_json_show_sanitize)
+expected='[[[{"id": "foo@three.com", "match": true, "excluded": false,
+ "filename": "YYYYY",
+ "timestamp": 978709437, "date_relative": "2001-01-05", "tags": ["inbox", "unread"],
+ "headers": {"Subject": "three",
+ "From": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "To": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "Date": "Fri, 05 Jan 2001 15:43:57 +0000"}, "body": [{"id": 1,
+ "content-type": "text/plain", "content": "This is just a test message (#5)\n"}]},
+ [[{"id": "msg-006@notmuch-test-suite", "match": true, "excluded": false,
+ "filename": "YYYYY",
+ "timestamp": 978709437, "date_relative": "2001-01-05", "tags": ["inbox", "unread"],
+ "headers": {"Subject": "Re: three",
+ "From": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "To": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "Date": "Fri, 05 Jan 2001 15:43:57 +0000"}, "body": [{"id": 1,
+ "content-type": "text/plain", "content": "This is just a test message (#6)\n"}]},
+ []]]]]]'
+expected=`echo "$expected" | notmuch_json_show_sanitize`
+test_expect_equal_json "$output" "$expected"
+
+test_begin_subtest "Use last Reference"
+test_subtest_known_broken
+add_message '[id]="foo@four.com"' \
+    '[subject]="four"'
+add_message '[id]="bar@four.com"' \
+    '[subject]="not-four"'
+add_message '[in-reply-to]="<baz@four.com>"' \
+    '[references]="<baz@four.com> <foo@four.com>"' \
+    '[subject]="neither"'
+output=$(notmuch show --format=json 'subject:four' | notmuch_json_show_sanitize)
+expected='[[[{"id": "foo@four.com", "match": true, "excluded": false,
+ "filename": "YYYYY",
+ "timestamp": 978709437, "date_relative": "2001-01-05", "tags": ["inbox", "unread"],
+ "headers": {"Subject": "four",
+ "From": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "To": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "Date": "Fri, 05 Jan 2001 15:43:57 +0000"}, "body": [{"id": 1,
+ "content-type": "text/plain", "content": "This is just a test message (#7)\n"}]},
+ [[{"id": "msg-009@notmuch-test-suite", "match": false, "excluded": false,
+ "filename": "YYYYY",
+ "timestamp": 978709437, "date_relative": "2001-01-05", "tags": ["inbox", "unread"],
+ "headers": {"Subject": "neither",
+ "From": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "To": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "Date": "Fri, 05 Jan 2001 15:43:57 +0000"}, "body": [{"id": 1,
+ "content-type": "text/plain", "content": "This is just a test message (#9)\n"}]},
+ []]]]], [[{"id": "bar@four.com", "match": true, "excluded": false,
+ "filename": "YYYYY",
+ "timestamp": 978709437, "date_relative": "2001-01-05", "tags": ["inbox", "unread"],
+ "headers": {"Subject": "not-four",
+ "From": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "To": "Notmuch Test Suite <test_suite@notmuchmail.org>",
+ "Date": "Fri, 05 Jan 2001 15:43:57 +0000"}, "body": [{"id": 1,
+ "content-type": "text/plain", "content": "This is just a test message (#8)\n"}]}, []]]]'
+expected=`echo "$expected" | notmuch_json_show_sanitize`
+test_expect_equal_json "$output" "$expected"
+
+
+test_done