Abstract: Novel sequence tagged sites (STSs), probes and primers useful, e.g., for detecting the presence or absence of an STS in a sample, and methods of using these STSs, probes and primers, e.g., in methods of detecting alterations in the Y chromosome are disclosed. These compositions are also useful in methods of diagnosing or aiding in the diagnosis and/or cause of reduced sperm count and in methods of predicting or aiding in the prediction of the likelihood of success of infertility treatments.