Early infant HIV diagnosis and antiretroviral therapy (ART) initiation are now implemented shortly after birth. Maintaining and monitoring ART adherence is difficult and requires frequent visits. We, therefore, investigated whether HIV antibodies and HIV-1 DNA levels are markers of cumulative viremia. We conducted a cross sectional investigation at 2 years of age of HIV antibodies and HIV-1 DNA levels in a well characterized cohort of 31 children who started ART shortly after birth. HIV antibodies were measured by a combination of the Abbott ARCHITECT HIV Ag/Ab Combo and Geenius HIV 1/2 supplemental assays; and total HIV-1 DNA quantified using a sensitive quantitative PCR (qPCR) assay targeting the HIV-1 integrase gene. Infant post-exposure prophylaxis consisted of zidovudine (AZT) and nevirapine (NPV) (or NVP only, in one child) within 1 day of birth, transitioning, after positive diagnosis, to three-drug ART, at a median [interquartile range (IQR)] of 7 (4-9.5) days. Twelve of 31 children had well suppressed HIV plasma viral loads (HIVVL) and the remainder periods of viremia (HIVVL > 100 copies/ml after 3 months of ART), classified as non-suppressed. At 24 months of age: 11 of 12 (92%) of well suppressed children had undetectable HIV-1 antibodies versus 3 of 19 (16%) non-suppressed children (P < 0.001) and 7 of 12 (58%) well suppressed children had undetectable HIV-1 DNA versus 3 of 19 (16%) non-suppressed children (P = 0.02). Considering low assay costs and the high proportion of well suppressed children with undetected antibody levels at 2 years, HIV antibody levels may be a valuable marker of cumulative adherence in children who start treatment shortly after birth and could prompt adherence and viral load investigation.