Mice are widely used as experimental models due to several positive characteristics and in particular their suitability for studies involving molecular biology and transgenesis. Despite the large number of mice strains currently available, the literature regarding their basic reproductive biology is still relatively scarce. Herein, we comparatively evaluated several important and correlated parameters related to testis structure and function in sexually mature male mice of inbred (C57BL/6, n = 19; BALB/c, n = 17) and outbred (Swiss, n = 17) strains, frequently utilized in research. Swiss mice presented significant variation for many parameters evaluated, including higher sperm production, mainly when compared to the C57BL/6 strain. However, some key parameters such as the duration of spermatogenesis, the Sertoli cell number per testis, and the spermatogenic efficiency were similar among the different strains. Although presenting significantly higher Leydig cell (LC) proportion and numbers per testis gram and per testis, the anogenital index was smaller in Swiss mice. Estradiol levels were lower in C57BL/6, whereas testosterone levels and 3β-HSD expression were similar among strains. Regarding the LC/macrophages relationship, in comparison to the literature, we reported a much higher contribution of macrophages to the mouse intertubule. Thus, we estimated that there are around 1.6 macrophages per LC in BALB/c mice and this intriguing finding could be relevant to testis function in overall and spermatogonial biology in particular. Taken together, our results highlight the importance of knowing more accurately the testis structure and function in the different mice strains available for research, particularly when a specific testis parameter is being investigated.