During encounters with predators, prey that flee into refuges decide how long to hide. Refuge use theory predicts that hiding time increases as the risk of emerging increases. Lizards that escape by autotomizing their tails incur costs, including temporary decrease in speed and loss of ability to use autotomy. Thus, risk of being captured upon emergence is greater after autotomy. Also, a predator that captures a prey may later be assessed as posing greater threat. We predicted that hiding time increases after a lizard has been captured or has undergone autotomy. A previous study of striped plateau lizards (Sceloporus virgatus) showed that the proportion of lizards that entered refuges increased after autotomy but not after earlier capture. To examine unstudied effects of autotomy and capture on hiding time, we conducted a 2 × 2 factorial field experiment with handling and autotomy as factors. The four groups were (1) unhandled intact controls; (2) unhandled autotomized; (3) captured (and handled) intact, but not autotomized; and (4) captured, handled and autotomized. Because entering cool refuges entails costly decrease in body temperature, hiding times are shorter in cooler refuges. We controlled this effect statistically by conducting analyses of covariance incorporating difference in air temperature inside and outside refuges as the covariate. As predicted, autotomy and handling led to longer hiding times. However, handling affected hiding time only in intact lizards. Our results add autotomy and capture to risk factors known to affect hiding time, augmenting a growing body of knowledge supporting the hypothesis that trade-offs between costs of emerging and remaining in a refuge guide decisions about hiding time.