Trapping and handling is stressful for wild animals and may result in injuries. Minimizing stress and injuries is important not only for the welfare of the animals, but to assure integrity of research using trapped wild animals. By recording injury rates associated with trapping and handling, it is possible to assess the welfare performance of trapping and handling methods. Although the International Organization for Standardization published a standardized scale for the type and severity of injuries caused by trapping and handling (ISO 1999), it does not provide guidelines for acceptable standards of animal welfare; that is left to the researchers themselves to determine. The purpose of this paper is to measure the level of injury to wild squirrels caused by trapping and handling using minimally disruptive methods. We report our injury rates from several studies conducted in California, USA, that used various trapping and handling methods and the refined procedures we have adopted. Our data set on multiple Sciuridae species provides values for comparison with other studies. We found that using a canvas cover for traps minimized stress and injuries in captured squirrels. We also found that using a cone handling bag minimized handling time and stress associated with handling and eliminated the need for chemical immobilants. Further, we found that covering the animals' eyes during handling appeared to reduce visible signs of stress. © 2013 The Wildlife Society.