As part of a health survey of New Zealand sea lions (Phocarctos hookeri) on Enderby Island, Auckland Islands (50°30′S, 166°17′E), neonatal mortality was closely monitored at the Sandy Bay colony for seven consecutive years. Throughout the breeding seasons 1998–99 to 2004–05, more than 400 postmortem examinations were performed on pups found dead at this site. The primary causes of death were categorized as trauma (35%), bacterial infections (24%), hookworm infection (13%), starvation (13%), and stillbirth (4%). For most pups, more than one diagnosis was recorded. Every year, two distinct peaks of trauma were observed: the first associated with mature bulls fighting within the harem and the second with subadult males abducting pups. In 2001–02 and 2002–03, epidemics caused by Klebsiella pneumoniae increased mortality by three times the mean in nonepidemic years (10.2%). The increased mortality was attributed directly to acute suppurative infection due to the bacterium and also to an increase in traumatic deaths of debilitated pups. Parasitic infection with the hookworm Uncinaria spp. was a common finding in all pups older than three weeks of age and debilitation by the parasite may have contributed to increased susceptibility to other pathogens such as Klebsiella sp. or Salmonella sp. This study provides valuable quantitative data on the natural causes of neonatal mortality in New Zealand sea lions that can be used in demographic models for management of threatened species.