Malnutrition is a significant risk factor for childhood infectious diseases in developing countries, including PNG. Whilst the mechanisms are not fully understood there is little doubt that impairment of immune function is a major contributing factor in enhancing disease susceptibility in malnourished children. The aim of this study was to examine the ontogeny of the humoral immune system and the effect of undernutrition on the immune ontogeny profile in children less than 60 months of age. A prospective, cross-sectional study with measurements of nutritional status and parameters of the immune response being assessed simultaneously. The children within each group were stratified according to age for the purpose of comparative analysis. The children were from the Goroka region of the Eastern Highland Province of PNG and had been admitted to hospital with bacterial pneumonia. They were classified as undernourished (less than 80% weight for age) or nourished (greater than 80% weight for age). Serum albumin, IgG, IgA, IgM and salivary albumin and IgA were measured. Antibodies to nontypable Haemophilus influenzae outer membrane protein and Escherichia coli O antigen were also determined in serum and saliva. Lower values of salivary IgA were observed in infants and younger children (less than 13 months of age) with a larger number of children having no detectable IgA compared with older children. The ontogeny profile was similar in undernourished and nourished children. In nourished children the specific antibody profiles peaked earlier than IgA. At different age intervals the concentration of immunoglobulins in serum and saliva from children that were undernourished was found to be significantly decreased or not changed compared to nourished children. Generally undernourished children had lower levels of specific antibodies compared with nourished children. In conclusion, the effect of undernutrition on the humoral immune response is dependent on the age of the child.