The reduction of nesting habitat has likely contributed to the decline of Humboldt penguins in Peru. We investigated the effects of using different nesting sites and nest types on the breeding success of Humboldt penguins at Punta San Juan, the largest colony in Peru, between 1993 and 1996. The majority of penguins bred on cliff tops (72%) where breeding success was high (1.03-1.18 fledglings/nest). In contrast, penguins nesting on beaches had lower breeding success (0.44-1.1 fledglings/nest), with reproductive failure mostly due to nest flooding during ocean swell years. The breeding success of penguins using surface nests (1.02-1.07 fledglings/nest) was similar to that of those using burrows (0.89-0.97 fledglings/nest) and crevices (0.85-1.15 fledglings/nest) on cliff slopes and beaches, respectively. Nevertheless, on cliff tops where the main guano deposits are located, burrows were the most successful nests (1.41 fledglings/nest). Halting guano extraction around the main breeding areas may increase the availability of burrowing substrates and, thus breeding success of this endangered species. © 2001 Elsevier Science Ltd.