Ungulate mortality from capture-related injuries is a recurring concern for researchers and game managers throughout North America and elsewhere. We evaluated effects of 7 variables to determine whether ungulate mortality could be reduced by modifying capture and handling procedures during helicopter net-gunning. During winter 2001–2006, we captured 208 white-tailed deer (Odocoileus virginianus) and 281 pronghorn (Antilocapra americana) by helicopter net-gunning throughout the Northern Great Plains. Of 281 pronghorn, 25 (8.9%) died from capture-related injuries; 12 were from direct injuries during capture, and 13 occurred postrelease. Of 208 deer, 3 (1.4%) died from injuries sustained during helicopter captures, with no mortalities documented postrelease. We used logistic regression to evaluate the probability that ungulates would die of injuries associated with helicopter net-gun captures by analyzing effects of snow depth, transport distance, ambient and rectal temperatures, pursuit and handling times, and whether individuals were transported to processing sites. The probability of capture-related mortality postrelease decreased 58% when transport distance was reduced from 14.5 km to 0 km and by 69% when pursuit time decreased from 9 minutes to <1 minute. Wildlife managers and researchers using helicopter capture services in landscapes of the Midwest should limit pursuit time and eliminate animal transport during pronghorn and white-tailed deer capture operations to minimize mortality rates postrelease.