Field studies often use external examination of the vagina or the swelling of the scrotum to make deductions about the reproductive condition of rodents. In this study we sought to determine what information on reproductive condition could be gained from external examination of the reproductive anatomy of spinifex hopping mice (Notomys alexis) using individuals from a captive colony. Female N. alexis with perforate vaginae had a significantly larger mean uterine mass and larger mean maximum ovarian follicle diameter than non-perforate females. Corpora lutea were recorded in two perforate animals but were not present in females with a 'pinhole'-size perforate or non-perforate vagina. In male hopping mice scrotal bulge size was unrelated to testes mass, ventral prostate mass or presence/absence of sperm in the cauda epididymides. Males with dark scrotal pigmentation had a significantly smaller mean testes mass than males with light or no pigmentation. However, there was no relationship between scrotal pigmentation and ventral prostate mass or sperm presence in the cauda epididymides. Our study suggests that vaginal perforation is an acceptable indicator of sexual maturity in female hopping mice, but scrotal bulge size and scrotal pigmentation should not be used to predict reproductive condition of males.