Researchers often consider the importance of minimizing holding time during research activities; however, the long-term costs of such handling stress is rarely measured explicitly. As part of an ongoing study of common eiders (Somateria mollissima) at a breeding colony in East Bay, Southampton Island, Nunavut, we recorded duration of restraint for females captured during avian cholera epizootics (2007 and 2008) and monitored female fates (breeding probability, onset of laying, and survival) relative to holding time. Probability of death increased with holding time in 2007 from an estimated 0.05 for females held 20 min to 0.33 for females held for 150 min. In 2008, we responded by limiting holding time to <90 min and mortality was no longer positively correlated with holding time, although total mortality was greater due to increased severity of avian cholera. In both years, longer restraint durations delayed onset of egg-laying after capture by 0.5 days for each 10 min of additional restraint but did not prevent breeding. This delay of nest initiation did not enhance survival probability. Our results show that prolonged holding time can exacerbate mortality during epizootics and emphasize the importance of minimizing restraint time in wild birds, especially in the presence of diseases.