Objectives The influence of testosterone on the prostate and corpus cavernosum have been studied extensively. However, the influence of testosterone on the lower urinary tract (bladder and urethra) have not been investigated to any great extent. The aim of this study was to determine whether androgen deprivation alters lower urinary tract metabolism. Methods A total of 16 rabbits were divided into four groups of four rabbits each. Each rabbit in groups 1-3 underwent surgical bilateral castration for duration of 1, 2, and 4 weeks, and group 4 underwent sham operations. Sections of bladder body and base wall and mucosa, urethra and corpora were isolated, frozen, and stored under liquid nitrogen. The activities of citrate synthase-thapsigargin sensitive Ca2+ ATPase (Sarco/Endoplasmic Reticulum Ca2+ ATPase [SERCA]), and choline acetyl-transferase were examined as markers for mitochondrial function, sarcoplasmic reticular calcium storage and release, and cholinergic nerve function, respectively. Results The activity of SR function indicator, Ca2+ ATPase was significantly higher in the control corpora than in the control bladder or urethra. Castration resulted in decreased activity in the mitochondria specific enzyme, citrate synthase, the activity of which was greatest in the urethra and lowest in the corpora. Cholinergic nerve density indicator, choline acetyltransferase activity was greatest in the bladder body and lowest in the urethra. Conclusions Our data indicate that (1) significant differences exist in the activities of all three enzymes in the various organs associated with the lower urinary tract; and (2) that castration results in significant alterations in the activities of all three enzymes in the bladder body, base, urethra, and corpora.