We assessed the prevalence of vitamin D deficiency among 101 perinatally HIV-infected Thai adolescents receiving antiretroviral therapy. Median age was 14.3 (interquartile range 13.0–15.7) years, and 90% had a HIV RNA <50 copies/mL. The median (interquartile range) 25-hydroxyvitamin D (25-OHD) level was 24.8 (6.9–46.9) ng/mL; 25 (24.7%) had vitamin D deficiency (25-OHD <20 ng/mL) and 47 (46.5%) had insufficiency (25-OHD 20–30 ng/mL). Adolescents with vitamin D deficiency had significantly higher parathyroid hormone levels (54.9 vs. 40.2 pg/mL, P < 0.007). No associations between vitamin D deficiency and body mass index, bone mineral density, efavirenz use, HIV RNA, CD4 or self-reported sunlight exposure were observed.