Zidovudine (AZT) lowers the perinatal transmission of HIV but can impair mitochondrial function by depleting mitochondrial DNA (mtDNA). AZT therapy and perinatal nutritional deprivation affect the body fat distribution, which influences glucose tolerance. We sought to determine whether intra-uterine exposure to AZT interacts with low protein diet to impact on birth weight and glucose homeostasis in the offspring. Pregnant mice and their offspring were given AZT a low protein diet (LPD) or both AZT and a low protein diet (LPD+AZT). AZT reduced mtDNA copy number in liver and birth weight in the offspring and increased their fasting glucose and insulin (p=0.021, 0.03, 0.001 and 0.011 respectively) at 6-8 weeks of age. LPD decreased litter size and birth weight (p=0.01 and 0.012). In the LPD+AZT group, birth weight and litter size were reduced compared with untreated controls and fasting blood glucose and insulin were raised. There was a significant interaction between LPD and AZT on fasting insulin levels (p=0.025). Islet size was not significantly affected, but the mean beta-cell area/islet was reduced in the LPD+AZT group compared to controls (P<0.05). Early exposure to AZT interacts with low protein diet to impair foetal development. This combination appeared to impair the supply of insulin and hence glucose homeostasis in the mouse, perhaps as a result of impaired mitochondrial function. While is in not certain that this can be extrapolated to humans, maternal nutritional deprivation combined with AIDS therapy could influence both birth weight and onset of diabetes.