The immature state of the immune system of neonates makes them vulnerable to infectious agents, including Streptococcus pneumoniae. The aim of our study was to analyse and compare the effects of Escherichia coli heat-labile enterototoxin (LT)-K63 and CpG2006 on cells and key molecules of the neonatal immune system, using a previously established immunization model with pneumococcal polysaccharide of serotype 1 conjugated to tetanus toxoid (TT) (Pnc1-TT). The cellular response was evaluated by measuring cytokine secretion and proliferation upon in vitro stimulation with TT, the protein moiety of Pnc1-TT, and antibody (Ab) to both the polysaccharide (PS) and protein parts of the vaccine were measured by enzyme-linked immunosorbent assay (ELISA). Antigen (Ag)-presenting and co-stimulatory capacity of neonatal B-cells was evaluated by staining for major histocompatibility complex (MHC)II, CD80, CD86 and CD40. The results showed that both LT-K63 and CpG2006 significantly enhanced the neonatal Ab response to Pnc1-TT. Spleen cells from mice receiving LT-K63 showed enhanced proliferation and interferon (IFN)-γ, interleukin (IL)-4, IL-5 and IL-10 secretion upon TT stimulation, whereas cells from mice receiving CpG2006 could only enhance IL-10 secretion. LT-K63 and to a lesser extent CpG2006 enhanced the capacity of B-cells to up-regulate the expression of co-stimulatory and activation markers compared with those of mice receiving Pnc1-TT alone. Thus, we conclude that LT-K63 markedly improves T-cell activation whereas the direct adjuvant effect of CpG2006 on neonatal B-cells may partly compensate for lower T-cell help resulting in enhanced neonatal Ab responses to both the TT and PS parts of the vaccine by both adjuvants.