In this study we examine physiological responses of Peruvian hake (Merluccius gayi peruanus) to changes in their population structure and physical environment during the period 1971-2004. In particular, we assess the relative investment of energy in growth and/or reproduction of small (20-35 cm) and large (35-50 cm) hake. We calculated the (i) condition (Fulton's K), (ii) gonad and (iii) gut fullness indices for 42,761 female hakes sampled from commercial landings; these indices indicate fish somatic, reproductive and feeding condition, respectively. Using Generalized Additive Models we then examined potential relationships between these indices and sea surface temperature anomalies and date. Drastic energy exhaustion and a decrease in female hake fecundity were observed during El Niño events. The long-term trend showed a general increase in condition factor and a decrease in gonad index for large hake between 1971 and 2004. Small hake exhibited a different trend with an increase in reproductive activity, which was accompanied by an earlier maturation. We hypothesise that the observed low investment of energy in reproduction by large female hake might be related to the lack of large males, due to a sex-selective fishery and the impact of El Niño. We suggest that fishing diminished hake reproductive capacity, modified the sex ratio in favour of females and increased population vulnerability to environmental stress, in particular to the El Niño. The impact of multidecadal variability and predators like the squid, Dosidicus gigas, remain unresolved until longer time series become available. © 2008 Elsevier Ltd. All rights reserved.