The precise identity of spermatogonial stem cells—the germline stem cell of the adult testis—remains a controversial topic. Technical limitations have included the lack of specific markers and methods for lineage tracing of Asingle spermatogonia and their subsets. Immunolocalization of proteins in tissue sections has been a standard tool for the in situ identification and visualization of rare cellular subsets. However, these studies are limited by the need for faithful and reliable protein markers to define these cell types, as well as the availability of specific antibodies to these markers. Here we describe the use of a monoclonal antibody to Pax7 as a means to detect spermatogonial stem cells (SSCs) both in tissue sections and in intact seminiferous tubules. Furthermore, we describe methods for lineage tracing as an alternative method to visualize Pax7+ spermatogonial stem cells and their progeny.