Male Antechinus stuartii (Marsupialia: Dasyuridae) undergo significant endocrinological changes during their life history. The endocrine changes are associated with complete male mortality. The accessory reproductive tract of males is important for seminal plasma production, and changes associated with the reproductive cycle were not described in detail by earlier studies. The present study sought to describe some of the seasonal changes in structure of the male accessory reproductive tract in relation to the known hormonal changes. The epididymis, prostate, and bulbourethral glands are relatively undifferentiated in February and May, a time when plasma concentrations of testosterone are known to be low. By July, considerable hypertrophy and differentiation of the accessory reproductive tract are observed. This is most obvious in the bulbourethral glands, which change from being indistinguishable from one another in February and May to being three large morphologically and histologically distinct glands in July. The hypertrophy and secretory activity continue into August, the breeding season. These findings correlate with the hormonal profiles found in other studies of A. stuartii. J Morphol 231:261–275, 1997. © 1997 Wiley‐Liss, Inc.