Objective To explore the effect of different delivery modes, vaginal delivery compared to caesarean section with or without initiation of labour, on the immune system and brain of the infants. Further, we aimed to elucidate gender and gestational ages’ effect on these biomarkers. Design Retrospective case control study Setting Dried blood spots from new-born screening biobank drawn 2-4 days after birth Population or Sample Mature new-borns divided into delivery by pre-labour (n=714), in-labour caesarean section (n=655), and vaginally (n=5897). Method The samples were analysed for inflammatory markers (IL-18, MCP-1, CRP, sTNF RI), stress- (HSP-70), growth- (EGF, VEGF-A), and neurotrophic factors (BDNF, NT-3, S100B). Main Outcome Measures Delivery by caesarean section with or without initiation of labour Results The neonatal levels of inflammatory and stress-markers were significantly lower, while the levels of growth factors were higher after pre-labour caesarean section compared to vaginal delivery. The biomarker levels were similar after in-labour caesarean section and vaginal delivery. Males had generally higher levels of inflammation and lower levels of growth and neurotrophic factors. Overall, the levels of inflammatory markers increased, and the growth factors decreased with increasing gestational age. Conclusion The biomarker levels indicates that the labour process has an important effect on the foetal immune system and level of stress, regardless if the delivery ends with caesarean section or vaginal birth. Funding ”Læge Sofus Carl Emil Friis og hustru Olga Doris Friis’ legat” and ”Fonden til Lægevidenskabens Fremme”. Keywords Inflammation; brain; CODIBINE; caesarean section; dried blood spot samples