Grey seal pup mortality was studied on three islands in the Outer Hebrides; North Rona, an inland breeding colony; Ceann Ear in the Monach archipelago, a sand beach breeding group; and Shillay in the Sound of Harris where both types of environment are represented. The overall mortality rates were broadly similar, ranging from 14.3 to 23.2%, but the primary causes of death varied greatly in importance on the different islands. On North Rona starvation and infection were the major causes of mortality and on the Monach Isles washing off and starvation were the two principal causes of loss. On the inland sites on Shillay infections were the major cause of death, whereas on the beaches starvation was the single most important cause of mortality. Some data on morbidity, principally due to conjunctivitis and infected wounds, are presented. Infectious agents, mainly various species of Streptococci and Corynebacterium, were found to be island‐specific to some degree. The adult seals, rather than other aspects of the environment, were found to carry the pathogens involved and seal pups were found to be immunologically deficient.