Individual identification (ID) of animals is important in scientific studies and considered as routine management. The present study evaluated acute effects of the ID methods partial toe amputation (TOE), ear tagging (TAG) and ear punching (PUNCH) in preweaning mice. Ten litters of the FVB/N strain were used (83 pups). Two pups per litter were assigned to each of the three methods and two pups per litter were controls. The morphological, motor and behavioural development of the pups was monitored from birth (day 1). TOE was performed day 7 or 8 by cutting one toe at the distal part of the second phalangeal bone using sharp scissors. TAG was performed day 19 by attaching a metal ear tag to the pinna. PUNCH was performed day 19 by punching a hole on the edge of the pinna. The reaction of the pup during and after the procedure was observed. At weaning (day 21), a clinical examination was performed on all pups, completed with the Novel Cage behavioural test. The strongest reaction to the ID procedure was found in TAG animals and 62 % of the pups vocalised during the procedure. Common behaviours were struggling, shaking and jumping. The pinna was red and swollen for three days after the procedure. In the PUNCH group 19 % of the pups vocalised during the procedure and behaviours observed were scratching the ear and occasional freezing. In the TOE group, 29 % of the pups vocalised during the procedure. In the cage they crawled into the nest and one pup licked the toe. The amputated toes were swollen for about three days. The main findings in the clinical examination were that none of the ID methods affected gait, grip strength or balance in the pups. However, TAG pups had abnormal body posture with heads tilted to one side.