Introduction: Deficiencies of micronutrients play a role in human immunodeficiency virus (HIV) infection and its severity. Identifying the micronutrient status would guide supplementation, thus altering the disease progression and severity. Material and methods: A cross-sectional hospital-based study was conducted in Southern India on hundred HIV-infected children. Estimation of serum micronutrient levels (zinc, copper, and iron) and comparison of the deficient micronutrients with clinical stages, immunological categories, CD4 counts, and nutritional status was performed. Results: Among 100 HIV-infected children, zinc deficiency was the most common (62%), whereas copper and iron deficiency was present in 2% and 1%, respectively. Mean age of children was 11.20 ± 3.14 years, 52% were girls, 24% were malnourished, 76% were receiving antiretroviral therapy (ART), and four had CD4 counts < 200/mm 2 indicating AIDS. Using Kruskalwallis test, serum iron levels (p = 0.000) and CD4 levels (p = 0.001) were significantly associated with clinical stages, while serum zinc levels (p = 0.043) and CD4 levels (p = 0.000) were significantly associated with various degrees of immune classification. Mean micronutrient levels did not correlate significantly with CD4 counts less than and greater than 350 by unpaired t test. Zinc deficiency did not correlate with clinical staging, immunological classification, nutritional status, and receipt of ART on multiple logistic regression analysis. Conclusion: In HIV-infected children, zinc deficiency was the most common and it did not correlate with clinical staging, immunological classification, nutritional status, and receipt of antiretroviral therapy. Hence, supplementation of zinc would be required along with initiation of ART.