The status of the Humboldt Penguin (Spheniscus humboldti) was investigated in Peru after the 1997-98 El Niño event, the strongest of the last century. Penguin numbers along the southern and central coast of Peru (97% of the total) did not differ significantly between 1999 and 2000; the average number was 4,425 individuals. In 1999, the proportion of juveniles (one-year-old birds) was only 0.2% compared with 7% in 2000, probably as a result of the 1997-98 El Niño. Penguins were found from La Foca Island (512’S) to Punta Coles (1742’S). However, the majority (78%) were clustered in five localities, Punta San Juan (36%), San Juanito Islet (11%), Hornillos Island (10%), Pachacamac Island (12%) and Tres Puertas (9%). The size and distribution of penguin colonies have changed over the last 15 years. Penguins have abandoned sites at Punta Corio, Sombrerillo and Morro Sama, and have decreased significantly in numbers in Punta San Fernando and Punta La Chira, where human disturbance has increased, mainly due to local fisheries activities. Penguins have increased at Punta San Juan, San Juanito Islet and San Gallan Island, all of which are partially protected. Half of the penguins were located in guano bird reserves, primarily at Punta San Juan. Guano bird reserves provide some protection against terrestrial predators and human disturbance; however, periodical guano extraction decreases their breeding success. Most penguin sites were found in inaccessible and marginal areas, which were vulnerable to occasional and unpredictable flooding from ocean swells. The methodology recommended by the Population and Habitat Viability Assessment workshop for a consistent census of penguins in Peru and Chile during the molting period was validated at the Punta San Juan Reserve. Continued monitoring of Humboldt Penguin numbers is recommended in order to more fully understand patterns of fluctuation and to be able to detect changes of conservation concern as early as possible. Collaborative efforts between local authorities and conservation biologists are needed to monitor and protect this vulnerable species.