There is increasing evidence that the functional state of the immune system at birth is predictive of the kinetics of immune maturation in early infancy. Moreover, this maturation process can have a major impact on early vaccine responses and can be a key determinant of risk for communicable and non-communicable diseases in later life. We hypothesize that environmental and genetic factors that are often typical for poor-resource countries may have an important impact on prenatal immune development and predispose populations in low-income settings to different vaccine responses and disease risks, compared to those living in high-income countries. In this paper we aimed to summarize the major differences between neonatal and adult immune function and describe what is known so far about discrepancies in immune function between newborns in high- and low-income settings. Further, we discuss the need to test the immunological feasibility of accelerated vaccination schedules in high-risk populations and the potential of variation in disease specific and non-specific vaccine effects.