For over a half century the ACI (August × Copenhagen) rat has been a primary model for studying renal agenesis and ipsilateral hypoplasia (IHP) of the Wolffian derived structures (WDS). Because the ACI rat is also used as a model for prostate research it is important to examine the relationship of IHP and urogenital sinus development. The prostate is dependent on androgens for proper growth and differentiation. Alteration in androgen production and/or delivery to the urogenital sinus has the potential to perturbate normal development. In this study we investigate whether the ipsilateral loss of the WDS is associated with altered prostate development. Digital images of serial sectioned fetal ACI rat urogenital sinus (UGS) were used to create 3-dimensional surface-rendered models of the developing prostate, seminal vesicle, vas deferens and utricle on gestational day 21. The number and volume of prostate ducts developing from the UGS were calculated from the 3-D model data. Animals exhibiting IHP had a significant decrease in total fetal prostate volume (40%; p<0.005) with significant regional specific differences when compared to normal male ACI rats. Anatomical and histological differences in the utricle, abnormal histology of the ipsilateral testes, and a truncation of the ipsilateral Wolffian ductal mesenchyme were also seen in the animals with IHP. Additional research is needed to further understand the mechanisms and consequences of IHP on prostate growth and development. Alterations to normal prenatal development of the male accessory sex organs can have important consequences for the growth and morphology of the adult gland.