The associations of Cesarean delivery with offspring metabolic and immune-mediated diseases are believed to derive from lack of mother-to-newborn transmission of specific microbes at birth. Bifidobacterium spp., in particular, has been hypothesized to play a health-promoting role, yet little is known about how delivery mode modifies colonization of the newborn by this group of microbes. The aim of this research was to examine the presence of Bifidobacterium in meconium and in the transitional stool, and to assess cytokine levels and hematological parameters in the venous cord blood of infants born by elective, pre-labor Cesarean section vs. vaginal delivery in Southern Brazil. We recruited 89 mother-newborn pairs (23 vaginal delivery and 66 elective cesarean delivery), obtained demographic information from a structured questionnaire and clinical information from medical records. We obtained umbilical cord venous blood and meconium samples following delivery and the transitional stool (the first defecation after meconium) before discharge. We determined plasma levels of IL-1β, IL-10, IL-6, GM-CSF, IL-5, IFN-γ, TNF-α, IL-2, IL-4 and IL-8 in the cord blood, and presence of stool Bifidobacterium by real time PCR. Compared to vaginally-delivered neonates, Cesarean-delivered neonates had a lower leukocyte count (p = 0.037), lower hemoglobin (p = 0.04), and lower levels of the cytokine GM-CSF (p = 0.009) in the cord blood. Moreover, Bifidobacterium was detected less often in the transitional stool of Cesarean-delivered neonates compared to vaginally-delivered neonates (p = 0.001). The results indicate that pre-labor Cesarean birth may be associated with microbial and hematological alterations in the neonate. The clinical significance of these findings remains to be determined in larger prospective birth cohort studies.