Inspiration of air containing high concentrations of carbon dioxide (CO2; hypercarbic gas exposure) mobilizes respiratory, sympathetic and hypothalamic-pituitary-adrenal axis responses and increases anxiety-like behaviour in rats and humans. Meanwhile the same stimulus induces panic attacks in the majority of panic disorder patients. However, little is known about the neural circuits that regulate these acute effects. In order to determine the effects of acute hypercarbic gas exposure on forebrain and brainstem circuits, conscious adult male rats were placed in flow cages and exposed to either atmospheric air or increasing environmental CO2 concentrations (from baseline concentrations up to 20 CO2) during a 5 min period. The presence of immunoreactivity for the protein product of the immediate-early gene c-fos was used as a measure of functional cellular responses. Exposing rats to hypercarbic gas increased anxiety-related behaviour and increased numbers of c-Fos-immunoreactive cells in subcortical regions of the brain involved in: (1) the initiation of fear- or anxiety-associated behavioural responses (i.e. the dorsomedial hypothalamus, perifornical nucleus and dorsolateral and ventrolateral periaqueductal gray); (2) mobilization of the hypothalamic-pituitary-adrenal axis (i.e. the dorsomedial hypothalamus, perifornical nucleus and paraventricular hypothalamic nucleus); and (3) initiation of stress-related sympathetic responses (i.e. the dorsomedial hypothalamus, dorsolateral periaqueductal grey and rostroventrolateral medulla). These findings have implications for understanding how the brain senses changes in environmental CO2 concentrations and the neural mechanisms underlying the subsequent adaptive changes in stress-related physiology and behaviour.