The amygdala is mostly thought to exert an excitatory influence on the hypothalamic-pituitary-adrenal (HPA) axis, although its role regulating HPA basal tone is less clear, particularly during primate development. The current study examined the effects of neonatal amygdala lesions on basal HPA function and the postnatal testosterone (T) surge of rhesus monkeys reared with their mothers in large outdoor social groups. An early morning basal blood sample was collected at 2.5 months of age, whereas at 5 months samples were collected not only at sunrise, but also at mid-day and sunset to examine the diurnal rhythm of cortisol. At 2.5 months of age sham-operated males exhibited higher cortisol than females, but this sex difference was abolished by neonatal amygdalectomy, with lesioned males also showing lower basal cortisol than controls. Although neonatal amygdalectomy did not alter the postnatal T surge, there was a positive relationship between T and basal cortisol levels. At 5 months of age, neither the sex difference in cortisol, nor its correlation with T levels were apparent any longer. Instead, the diurnal cortisol rhythm of both males and females with amygdalectomy showed a blunted decline from mid-day to sunset compared to controls. These results indicate that neonatal amygdala damage alters basal HPA function in infant rhesus monkeys, affecting males only at early ages (at 2.5 months), while leaving the postnatal T surge intact, and resulting in a flattened diurnal rhythm in both genders at the later ages. Thus, the primate amygdala has a critical influence on the HPA axis in the first few months of life.