We report on the geographic and temporal variation in pup condition in 20 colonies of New Zealand fur seals Arctocephalus forsteri around South Island, New Zealand during three consecutive breeding seasons, 1996–98 (n = 6856 pups) and provide hypotheses to explain the observed patterns. Three alternative data combinations are presented to calculate pup condition from body measurements and identify which combination seems to be best suited for analysing geographic patterns. A morphometric index of pup condition was best estimated by comparing all pups in all years using least-squares linear regression of the loge-transformed measurements of length vs mass. Condition varied significantly among years and colonies, but not between sexes. We also estimated seasonal changes in pup densities at colonies and investigated the relationship between pup density and condition. Mean pup densities among colonies ranged from 4.94 to 7.46 pups/100 m2 (summer) and from 4.99 to 7.04 pups/100 m2 (winter) from 1996–98, and differences between summer and winter densities varied with year. Pup density explained a significant proportion of the variation in pup condition in 1996 and 1998, suggesting that condition is partly density-dependent. After accounting for the effect of density, we found geographic differences in pup condition, and we offer alternative hypotheses to explain these differences. We also show that the 1998 El Niño coincided with a reduction in pup condition. A morphometric index of pup condition seems to be useful as an indicator of spatial and temporal variation in the marine environment.