The Collaborative International Dictionary of English v.0.48:

Transept \Tran"sept\, n. [Pref. trans- + L. septum an inclosure.
   See Septum.] (Arch.)
   The transversal part of a church, which crosses at right
   angles to the greatest length, and between the nave and
   choir. In the basilicas, this had often no projection at its
   two ends. In Gothic churches these project these project
   greatly, and should be called the arms of the transept. It is
   common, however, to speak of the arms themselves as the
   transepts.
   [1913 Webster]

WordNet (r) 3.0 (2006):

transept
    n 1: structure forming the transverse part of a cruciform
         church; crosses the nave at right angles

Moby Thesaurus II by Grady Ward, 1.0:

35 Moby Thesaurus words for "transept":
   Easter sepulcher, ambry, apse, baptistery, blindstory, chancel,
   choir, cloisters, confessional, confessionary, cross bitt,
   crossarm, crossbar, crosspiece, crypt, diaconicon, diaconicum,
   doubletree, nave, porch, presbytery, rood loft, rood stair,
   rood tower, sacrarium, sacristy, singletree, swingletree, transom,
   transversal, transverse, traverse, triforium, vestry,
   whippletree