Between April and October 2003–2004, the changes in occupation of three bat boxes used by Pipistrellus pygmaeus were studied using a passive IR monitors and data loggers. Bat boxes were situated in a floodplain forest in south-eastern Moravia. Generalized additive models indicated that internal humidity described better the fluctuation in bat numbers during pregnancy and lactation than did changes in the internal temperature. Three variables (internal humidity, external temperature, and number of bats) described 87% of the variability in internal roost temperature, while the number of bats described only 29% of the variability. A negative correlation was found between the internal temperature and the number of bats roosting in a bat box the next day during pregnancy and lactation. The number of bats was also positively correlated with the internal humidity. The internal temperature of a roost with bats was biased by temperature strategies induced by the bats during particular reproductive periods. Mean temperature of occupied bat boxes was higher during pregnancy than during lactation. Females were able to go into torpor even during lactation period.