In this combined field and laboratory study, we assessed whether populations of native walleye in the Upper Mississippi River experienced altered genetic diversity correlated with exposure to estrogenic endocrine-active compounds (EACs). We collected fin-clips for genetic analysis from almost 600 walleye (13 sites) and subsampled 377 of these fish (6 sites) for blood and reproductive organs. Finally, we caged male fathead minnows at 5 sampling sites to confirm the presence of estrogenic EACs. Our findings indicate that male walleye in four river segments produced measurable concentrations of plasma vitellogenin (an egg-yolk protein and, when expressed in male fish, a biomarker of acute estrogenic exposure), a finding consistent with the presence of estrogenic EACs and consistent with published historical data for at least three of these study sites (Grand Rapids, St. Paul, and Lake City on Lake Pepin). Patterns of vitellogenin induction were consistent for native walleye and caged fathead minnows. No widespread occurrence of histopathological changes, such as intersex was found compared with published reports of intersex at the furthest downstream study site. To assess possible effects of estrogenic exposure on the genetic diversity of walleye populations at the study sites, we DNA-fingerprinted individual fish using 10 microsatellite loci. Genetic differences were observed between populations; however, these differences were consistent with geographic distance between populations, with the largest observed difference in genetic diversity found between fish upstream and downstream of St. Anthony Falls (and/or Lock and Dam 1 of the Mississippi River), traditionally a historical barrier to upstream fish movement. Although the persistent occurrence of endocrine disruption in wild fish populations is troubling, we did not detect degradation of reproductive organs in individual walleye or alteration in genetic diversity of walleye populations.