Live-capture is a necessary component for the scientific study and management of most mammals, but it may negatively affect their health and physiology. We compared blood parameters related to the stress response (nominal base levels) from red squirrels Tamiasciurus hudsonicus after capture of up to 4.5 h in five different live trap models (Hava-hart, Sherman, Tomahawk 102, Tomahawk 103 and ‘Special Squirrel’ trap) with true base levels (obtained in less than three minutes). In addition, we evaluated the capture rate in the five trap models. We found that (1) prolonged time in live traps altered stress hormone concentrations compared with true base levels, but maximum corticosteroid-binding capacity was unaffected; (2) squirrels captured in a trap model with reduced visibility (a roof cover – Hava-hart) had significantly lower (c. 50%) mean free cortisol levels compared with those captured in a trap model with full visibility (Tomahawk 102), but all other blood parameters were similar; (3) cortisol levels and white blood cell counts (mainly neutrophil counts) were positively related to duration of capture; (4) a non-covered trap (Tomahawk 102) was most effective and fully covered trap (Sherman) was least effective at capturing squirrels. We discuss the use of effective, yet less stress-inducing trap models to mitigate the stress caused by live-capture on these animals. We conclude that covered traps such as the Hava-hart may reduce trap-induced stress in red squirrels, but at the same time also reduces their capture rates.