In recent years, neonatal vitamin A supplementation is considered as an essential infant-survival intervention but the evidence is not conclusive. This randomized controlled clinical trial was conducted to evaluate the effect of vitamin A on immune competence in early infancy. Results would provide a mechanistic basis for understanding the effect of this intervention on infant survival. Within 2 days of birth, infants born at one maternity clinic located in a poor slum area of Dhaka city were supplemented with either 50,000 IU vitamin A or placebo. Live attenuated oral polio vaccine (OPV) and BCG vaccine were provided after supplementation. Infants also receive diphtheria, pertussis, tetanus (TT), hepatitis B (HBV) and Haemophilus influenzae B vaccines (pentavalent combination) along with OPV at 6, 10 and 14 weeks of age. Infant thymus size, anthropometry, feeding practice and morbidity data were collected at regular interval. Infant blood samples were collected to determine T-cell-receptor excision circle (TREC), total, naïve and memory T cells and mucosal targeting lymphocytes including Treg cells. TT-, HBV-, BCG- and OPV-specific T cell blastogenic, cytokine and plasma cell antibody responses were also measured. In 16 mo enrollment period, 306 newborns, equal number of boys and girls, were enrolled. ~95% completed the 4-month follow-up period. Baseline characteristics are presented here. Anthropometry and immune assays with fresh blood samples were completed immediately while stored samples were analyzed in single batches at the end of the trial. Connecting different aspects of immunological data in early infancy will help elucidate immune competence for protecting infection. Trial registration ClinicalTrials.gov: NCT01583972.