MOTIVATION: Y-chromosome short tandem repeats (Y-STRs) are widely used for population studies, forensic purposes and, potentially, the study of disease, therefore knowledge of their mutation rate is valuable. Here we show a novel method for estimation of site-specific Y-STR mutation rates from partial phylogenetic information, via the maximum likelihood framework. RESULTS: Given Y-STR data classified into haplogroups, we de-scribe the likelihood of observed data, and develop optimization strategies for deriving maximum likelihood estimates of mutation rates. We apply our method to Y-STR data from two recent papers. We show that our estimates are comparable, often more accurate than those obtained in familial studies, although our data sample is much smaller, and was not collected specifically for our study. Furthermore, we obtain mutation rate estimates for DYS388, DYS426, DYS457, three STRs for which there were no mutation rate measures until now.