Caesarean delivery has been linked to a number of inflammatory conditions in childhood and adolescence. Yet the mechanisms underlying these associations and their generalizability across contexts with different postnatal feeding and pathogenic exposures remain unclear. This study tests the association between delivery type and three measures of immune function, inflammation, morbidity and leukocyte proportions, in Ecuadorian infants and children aged 6 months to 2 years. Data were collected from mother–child pairs participating in a nationally representative health and nutrition survey Encuesta Nacional de Salud y Nutricion (ENSANUT-ECU) conducted in 2012. The analytic sample includes 828 mothers and infants with delivery information and measured biomarkers. Poisson regression models were used to examine the association between delivery type and markers of immune function, controlling for maternal and infant characteristics, including age, sex, sociodemographic characteristics and medical indications. 40.8% (n=338) of sample infants and children were delivered by caesarean. Compared to those born vaginally, infants born by caesarean were less likely to have elevated C-reactive protein (CRP) [CRP>2 mg/l; risk ratio (RR): 0.76, 95% confidence interval (CI): 0.58–1.00] and more likely to have illness symptoms (RR: 1.22, 95% CI: 1.01–1.46) and elevated basophils (RR: 1.83, 95% CI: 1.03–3.25). No other immune cell proportions differed by delivery type. The results suggest that differences in the perinatal exposures accompanying caesarean delivery may alter immune development and function, particularly in the inflammatory response to infection and in cells involved in the allergic response, across infancy and early childhood. Understanding the pathways linking perinatal exposures to immune development is important for preventing the development of inflammatory conditions.