Neonatal handling alters the structure of maternal behavior and affects mother-pup bonding.

•Neonatal handling affects maternal care and alters mother–pups relationship.•Handling desynchronizes mother–pup interactions by changing maternal behavior sequence.•Neonatal handling induces sex-dependent changes in the nest odor preference.•Handling affects CREB and BDNF levels in pup's olfactory bulb, in a sex-specific manner.•Results suggest a differential olfactory learning and preference for nest odor in pups.