Objective Low birthweight is associated with a decreased risk of childhood leukemia and an increased risk of both cardiovascular disease and all‐cause mortality in adult life. Possible biological mediators include systemic innate immunity and inflammation. We tested the hypothesis that birthweight was inversely associated with serum high sensitivity C reactive protein assay (hsCRP), a measure of both innate immunity and systemic inflammation. Methods Data on birthweight and current anthropometric measures along with a range of exposures were collected at 1 and 3 years of age in a population‐based cohort study of young children living in Havana, Cuba. A total of 986 children aged 3‐years‐old provided blood samples that were analyzed for serum hsCRP levels. Results Nearly 49% of children had detectable hsCRP levels in their serum. Lower birthweight was linearly associated with the natural log of hsCRP levels (beta coefficient −0.70 mg L−1 per kg increase in birthweight, 95% CI: −1.34 to −0.06). This was attenuated but still present after adjustment for the child's sex and municipality (−0.65 mg L−1 per kg birthweight; 95% CI: −1.38 to +0.08). There were no associations between growth from birth or anthropometric measures at 3 years and systemic inflammation. Conclusions Birthweight was inversely associated with serum hsCRP levels in children aged 3 years living in Cuba. These observations provide a potential mechanism that is present at the age of 3 years to explain the association between low birthweight and both decreased childhood leukemia and increased cardiovascular disease in adults.