Efforts to enhance recovery of endangered Hawaiian monk seals (Monachus schauinslandi) require an understanding of factors influencing population dynamics. This study examines relationships between body condition and survival of monk seal pups at French Frigate Shoals and Laysan Island and El Niño events. Girth measurements and mass estimates were used as indicators of pup body condition, and survival was evaluated from weaning to age 2. Linear models and logistic regression analysis were used to evaluate El Niño effects. Temporal trends in mean girth, mass, and survival were identified at both study sites. After accounting for temporal trends, girths were 3.7 cm and 2.7 cm greater during El Niño years at French Frigate Shoals and Laysan Island, respectively. Average mass estimates were significantly greater during El Niño years at French Frigate Shoals (2.6 kg increase), but were not significantly different at Laysan Island (1.8 kg increase). Weaned pups born at French Frigate Shoals during El Niño years survived significantly better, but this effect was not detected at Laysan Island. El Niño events probably affect pup condition and survival, but these parameters need to be monitored during future El Niño events to clarify these relationships.