Aim: To correlate the absolute CD4 count, CD4% and HIV viral load with different clinical manifestations of HIV in antiretroviral-naive children. Setting: The paediatric and perinatal HIV clinic in a tertiary care hospital over a period of 4 years, from January 1999 to December 2003. Materials and Methods: A total of 92 highly active antiretroviral-naive, HIV-1-infected children were enrolled in a cross-sectional study. The clinical manifestations, age, sex and CDC classification of each patient were determined. CD4 count, CD4% and HIV- 1 viral load were estimated at presentation and correlated with various clinical manifestations of HIV disease. Results: CD4% was higher in infants(p < 0.001) and lower in children over 5 years of age (p=0.01). Boys had a higher absolute CD4 count than girls (769 +/- 517 vs 532 +/- 430 cells/mm(3), p=0.02). Patients with lymphadenopathy (n=43) had a high CD4 count (840 +/- 487 cells/mm(3), p=0.01) whereas patients with HIV cardiomyopathy (n=4) had low CD4 counts ( mean 182 cells/ mm 3, p=0.04). In patients with failure to thrive (n=29), the CD4% was low (14 +/- 9%, p50.02) and HIV-1 viral load was high (mean 4.5 x 10(5) copies/ml, p=0.03). CD4 count, CD4% and HIV viral load did not correlate with the stage of the disease as per the CDC classification. Conclusion: HIV viral load, CD4 cell count and CD4% vary with age and disease complications in HIV-infected children. However, CD4 count, CD4% and viral load did not correlate with CDC classification.