The objective of the study was to determine the prevalence of pediatric human immunodeficiency virus 1 (HIV-1) mucocutaneous manifestations in the era of highly active antiretroviral therapy (HAART). We conducted population-based, prospective, multicenter pediatric HIV-1 surveillance in 276 children with perinatally acquired HIV-1 from 1988 to 2009. Centers for Disease Control and Prevention (CDC)-defined HIV-1 related mucocutaneous conditions among the 276 children were: category A (n = 152), B (n = 60), and C (n = 1). Nearly half of the category A and B diagnoses (43.4% [66/152] and 35.0% [21/60], respectively) occurred in the first year of life, with 59.2% (90/152) and 61.7% (37/60), respectively, occurring in the first 2 years of life. The most frequent infectious diagnosis was oropharyngeal thrush (n = 117, 42.4%); the most common inflammatory diagnosis was diaper dermatitis (n = 71, 25.7%). There was a temporal decline in the prevalence of A (pre-HAART cohort, 123; post-HAART cohort, 29; p < 0.01) and B (pre-HAART, 55; post-HAART, 5; p < 0.01) mucocutaneous diagnoses. In children with perinatal HIV-1, there was a significant decline in CDC category A and B mucocutaneous diagnoses by temporal cohort, consistent with the introduction of antiretroviral medications and HAART. Clinical category A and B mucocutaneous diagnoses were most common in the first 2 years of life, emphasizing the importance of early HIV-1 testing and HAART initiation.