Spermatogonial stem cells (SSCs) comprise a small population of germ cells with self-renewal potential. Previous studies have shown that SSCs share several common features with stem cells in other self-renewing tissues, including surface markers and proliferative machinery. However, studies of SSCs are severely handicapped by the small number of SSCs and the lack of SSC-specific markers. In the present study, we examined the utility of CDy1 and Rh123, both of which are used for the collection of stem cells in several self-renewing tissues. CDy1 stained germline stem (GS) cells, cultured spermatogonia enriched for SSC activity, after in vitro incubation without exerting toxic effects. Unlike previously reported stem cell-specific dyes, CDy1 was also useful for enrichment of SSCs in both GS cell culture and mature adult testes. Spermatogonial transplantation showed that ∼1 in 66.7 cells exhibited SSC activity after CDH1-based magnetic cell selection and CDy1 staining. In contrast, although Rh123 was previously used successfully to collect SSCs from cryptorchid testes, it was not possible to recover SSCs from both GS cell cultures and wild-type testes. Thus, CDy1 staining will provide a useful strategy for the enrichment of SSCs and may be used in conjunction with other reagents for the enrichment of SSCs.