The formation of sperm by the testes through the process of spermatogenesis is highly radiosensitive and can be affected by environmental, occupational and therapeutic radiation exposures. In this study, we applied an ex vivo mouse testis organ culture as an experimental model of spermatogenesis to investigate the radiobiological effects and to demonstrate its feasibility as a tool to determine response to complex, modulated radiation fields. This model uses Acr-GFP transgenic mice, which express the marker green fluorescent proteins specific for meiosis to allow observation of functional changes in real-time that can be used to analyze radiation-induced changes in the process of spermatogenesis. Our results showed that the model can accurately reproduce radiation-induced male germ cell toxicity, such as temporary infertility and permanent sterility. Furthermore, using a monochromatic X-ray microbeam, we applied this model to investigate the effects of heterogeneous radiation fields on testis tissue ex vivo. Our model represents a unique application in the field, which offers significant potential for gaining further mechanistic insight into radiation effects on the process of spermatogenesis.