Medullary serotonergic (5-HT) neurons are implicated in central chemoreception and 5-HT abnormalities are present in many cases of the Sudden Infant Death Syndrome (SIDS). Mice with a targeted disruption of the serotonin transporter (5-HTT) develop in the presence of excess 5-HT in brain extracellular fluid (ecf). As adults they exhibit reduced 5-HT neuron activity and 5-HT1A receptor binding with varying changes in postsynaptic 5-HT receptor function. They exhibit behavioral phenotypes (anxiety, reduced aggression) but little is known about their control of breathing. We show that conscious adult male and female 5-HTT knockout mice breathing air at room temperature have a higher resting oxygen consumption, breathing frequency and ventilation but a normal body temperature and ventilation/oxygen consumption ratio (the ventilatory equivalent) compared to Wild Type (WT) controls. In hypercapnia, there is a reduced ventilatory response (expressed as the ventilation/oxygen consumption ratio) that is much more prominent in males (-68%) than females (-22%). In hypoxia, both males and females exhibit a higher ventilation, oxygen consumption and body temperature but their ventilation/oxygen consumption ratio is normal. We conclude that 5-HTT knockout mice have diminished function of the medullary 5-HT system, which is manifest most remarkably in a substantial loss of CO2 sensitivity predominantly in males. This finding supports the importance of medullary 5-HT neurons in central chemoreception. Females either rely less on 5-HT neurons in chemoreception or adapt more readily to the loss of 5-HT function. This genetic model allows examination of the role of excess 5-HT in ecf in the development of the control of breathing and central chemoreception, which may be pertinent to SIDS.