This study's purpose was to determine whether asthma medication use in HIV positive children is associated with human leukocyte antigen (HLA) alleles. We reviewed HLA and medication data collected during the Women and Infants Transmission Study for 124 HIV positive children and their mothers. Analysis revealed that HLA-A68 (P = 0.006) was independent and predictive for time to first asthma medication use. There was a preventive association of Cw6 (P = 0.008) with asthma time. Highly active antiretroviral therapy (HAART) was also associated with time to first asthma medication use (P = 0.05). HLA alleles may modulate risk of developing a need for asthma medications and seem to function independently of the actions of HAART therapy.