In a wide range of synaptopathies a sex/gender bias in prevalence and clinical course has been reported. Therefore, analysis of the synaptic proteinaceous inventory in different brain regions in males and females is very desirable in understanding the molecular basis of brain function and the etiology of its diseases. In this study we analyzed the synaptic proteome of the prefrontal cortex, hippocampus, striatum and cerebellum in male and female mice. Our efforts should serve as a neurobiological framework to better understand the regional and sex/gender-specific synaptic function both in health and disease.