Animal models, epidemiological studies and a small number of randomised controlled trials suggest that BCG might protect infants against diseases other than tuberculosis. The hypothesis remains contentious because a mechanism to explain such protection has not been proven in infants. Adult studies suggest that BCG acts via epigenetic modifications to ‘train’ the innate immune system, enhancing its pro-inflammatory cytokine response to non-tuberculous pathogens. This thesis describes two randomised controlled trials, in Uganda and The Gambia, of early vs. delayed BCG vaccination in neonates. These explored the impact of BCG on the innate immune system through; 1) histone modifications at the promoter region of pro-inflammatory cytokines, 2) in vitro pro-inflammatory cytokine production following non-specific stimulation and 3) the inflammatory-iron axis response following in vivo heterologous stimulation. Clinical data were collected to explore the global applicability of the non-specific effects of BCG. These studies showed that infants BCG vaccinated at birth had significantly reduced allcause infectious disease incidence in the first 6 weeks of life compared to infants who had not received BCG (Incidence Rate Ratio 0.71 95%CI (0.53-0.95)). This was particularly pronounced in male infants (IRR 0.57 (0.36-0.88)). A corresponding trend toward reduced H3K4me3 (stimulatory) and H3K9me3 (inhibitory) epigenetic modification at the promoter region of pro-inflammatory cytokines in PBMCs collected at 6 weeks of age from BCG vaccinated infants was demonstrated. This was most significant for H3K9me3 at the TNFα promoter region (p=0.001), suggesting a potential for greater cytokine production in response to heterologous pathogen challenge. Proinflammatory cytokine concentrations following in vitro and in vivo non-specific stimulation were significantly increased in BCG vaccinated male infants at the 6 week time-point subsequent to receipt of Expanded Programme of Immunisation vaccinations. This thesis, therefore, provides strong evidence for a beneficial nonspecific effect of BCG in healthy neonates, likely mediated through epigenetic training of the innate immune system.