The urgent need for alternative methods of obtaining clean energy has accelerated wind farm development worldwide. To determine the effects of these facilities on the biodiversity of resident species, we conducted a spatio-temporal measurement on the glucocorticoid contents of four species of frugivorous bats (Artibeus lituratus, A. jamaicensis, Sturnira parvidens, and S. hondurensis) in Oaxaca, Mexico to test for physiological stress. Bats were captured at two sites: one with wind farms and the other without. Blood and feces were collected and cortisol and corticosterone were measured by immunoassay. Glucocorticoid contents were not significantly different between sites with or without wind turbines for any of the four species, although they averaged higher at wind turbine sites. However, cortisol and corticosterone concentrations were different between the dry and rainy seasons. The elevated glucocorticoid levels during the dry season are possibly due to the high degree of physiological stress generated by their reproductive activity. In general, the four phyllostomid bat species found at the wind farms in Oaxaca seem to tolerate or are not adversely affected physiologically by the presence of wind turbines.