Individual differences in sleep patterns of children may have developmental origins. In the present study, two factors known to influence behavioural development, monoamine oxidase A (MAOA) genotype and prenatal Fe-deficient (ID) diet, were examined for their influences on sleep patterns in juvenile rhesus monkeys. Sleep patterns were assessed based on a threshold for inactivity as recorded by activity monitors. Pregnant monkeys were fed diets containing either 100 parts per million (ppm) Fe (Fe sufficient, IS) or 10 ppm Fe (ID). At 3–4 months of age, male offspring were genotyped for polymorphisms of the MAOA gene that lead to high or low transcription. At 1 and 2 years of age, sleep patterns were assessed. Several parameters of sleep architecture changed with age. At 1 year of age, monkeys with the low-MAOA genotype demonstrated a trend towards more sleep episodes at night compared with those with the high-MAOA genotype. When monkeys reached 2 years of age, prenatal ID reversed this trend; ID in the low-MAOA group resulted in sleep fragmentation, more awakenings at night and more sleep episodes during the day when compared with prenatal IS in this genotype. The ability to consolidate sleep during the dark cycle was disrupted by prenatal ID, specifically in monkeys with the low-MAOA genotype.