Background: Data on pediatric HIV in Peru are limited. The National Institute of Child Health (Instituto Nacional de Salud del Niño: INSN) cares for the most HIV-infected children under the age of 18 years in the country. We describe the outcomes of children seen at INSN's HIV clinic over the 10 years when antiretroviral therapy and prevention of mother-to-child transmission (PMTCT) interventions became available in 2004. Methods: We conducted a retrospective review of INSN HIV clinic patients between 2003 and 2012. Deidentified data were collected and analyzed. Results: A total of 280 children were included: 50.0% (140/280) were male; 80.0% (224/280) lived in metropolitan Lima. Perinatal transmission was the mode of HIV infection in 91.4% (256/280) of children. Only 17% (32/191) of mothers were known to be HIV-infected at delivery; of these mothers, 41% (13/32) were receiving antiretroviral therapy at delivery, 72% (23/32) delivered by Cesarean section and 47% (15/32) of their infants received antiretroviral prophylaxis. Median age at HIV diagnosis for all children was 35.7 months (interquartile range 14.5-76.8 months), and 67% (143/213) had advanced disease (clinical stage C). After HIV diagnosis, the most frequent hospitalization discharge diagnoses were bacterial pneumonia, chronic malnutrition, diarrhea, anemia and tuberculosis. Twenty-four patients (8.6%) died at a median age of 77.4 months. Conclusions: Most cases of pediatric HIV were acquired via perinatal transmission; few mothers were diagnosed before delivery; and among mothers with known HIV status, PMTCT was suboptimal even after national PMTCT policy was implemented. Most children were diagnosed with advanced disease. These findings underscore the need for improving early pediatric HIV diagnosis and treatment, as well as PMTCT strategies.