Prenatal exposure of animals to bacterial endotoxin is an experimental model of systemic maternal infection in the human pregnancy. Previous studies in the rat have demonstrated that such exposure is associated with long term alterations to hypothalamic pituitary adrenal (HPA) axis development. Typically, these animals display an elevated HPA response to stress in adulthood. As neural development is more similar in the human and the guinea pig than the rat, this study adopted a guinea pig model of pregnancy to explore the effects of endotoxin exposure on the HPA axis in the offspring. The offspring of dams exposed to endotoxin exhibited an attenuated cortisol response to the novel environment stress in the weaning period. The degree to which this cortisol response was both buffered by the mother's presence, and habituated to on repeated exposure, differed significantly between the prenatal treatment groups. In adulthood, a diminished cortisol response to the immune challenge was only evident in the female offspring, while both male and female offspring exhibited altered febrile responses. The results of the present study indicate that prenatal bacterial exposure in the guinea pig results in offspring with lower cortisol responses to stress in later life. These findings contrast past research that has used the rat to model pregnancy. As such, the use of the guinea pig to model infection may provide a useful alternative model of human pregnancy to explore programming effects.