Neonatal maternal separation (NMS) is a form of stress that exerts persistent, sex-specific effects on the hypoxic ventilatory response. Adult male rats previously subjected to NMS show a 25% increase in the response whereas NMS females show a response 30% lower than controls (Genest et al. 2004). To assess the extent to which NMS affects ventilatory control development, we tested the hypothesis that NMS alters the ventilatory response to hypercapnia in awake, unrestrained rats. Pups subjected to NMS were placed in a temperature and humidity controlled incubator 3h/day for 10 consecutive days (P3 to P12). Control pups were undisturbed. At adulthood (8 to 10 weeks old), rats were placed in a plethysmography chamber for measurement of ventilatory parameters under baseline and hypercapnic conditions (FI_CO2 = 0.05). After 20 minutes of hypercapnia, the minute ventilation response measured in NMS males was 47% less than controls, owing to a lower tidal volume response (22%). Conversely, females previously subjected to NMS showed minute ventilation and tidal volume responses 63 and 18 % larger than controls respectively. While a lower baseline minute ventilation contributes to this effect, the higher VE/VCO₂ response observed in NMS females suggest a greater responsiveness to CO₂/H⁺ in this group. We conclude that NMS exerts sex-specific effects on the hypercapnic ventilatory response and that the neural mechanisms affected by NMS likely differ from those involved in the hypoxic chemoreflex.