To determine whether infectious diseases might have contributed to the present-day decline of northern fur seals (Callorhinus ursinus), preweaned pups (n=2,735), subadult males (n=98), and adults (n=179) were examined postmortem from 1986 to 2006 on St. Paul Island, Alaska. Gross necropsy findings and histologic lesions were used to determine causes of death. Five general categories of mortality were identified for pups: emaciation (1,454 pups, 53%), trauma (497 pups, 18%), perinatal mortality (516 pups, 19%), infectious diseases (82 pups, 3%), and miscellaneous causes (186 pups, 7%). A condition of unknown etiology characterized by multifocal necrotizing myopathy and cardiomyopathy was found in 92 pups. Thirty-three congenital anomalies were identified in 49 pups, including a rare multicentric ganglioneuro-blastoma. General linear models were used to examine change in pup mortality and condition (i.e., pup mass) over time. The prevalence of perinatal mortality appeared to increase during the study and relative to past reports. Trauma and infectious conditions appeared to decrease slightly from 1986 to 2006. Although relatively stable during this investigation, emaciation was greater than that reported for past studies. Emaciated pups weighed less than expected during 1988, 1996, and 2004 and more than expected during 1987, 1989, 1990, and 1994 (P≤0.003). Average annual weights for all other categories of mortality did not change significantly from 1986 to 2006. Fatal conditions for subadult males included hyperthermia, blunt trauma, entanglement, and bite wounds; nonfatal conditions included seizures, orange discoloration of the blubber, neoplasia, and parasitism. Causes of mortality for most adults included bite wounds with cellulitis and secondary infections, pulmonary edema, dystocia, blunt trauma, and neoplasia. We found no evidence to implicate infectious diseases as a cause in the recent decline of northern fur seals.