This study investigated breathing behavior in an odor – CO2-inhalation fear conditioning paradigm. A differential conditioning paradigm was applied in 55 participants. Both acquisition and extinction consisted of 3 CS+ and 3 CS- trials. Diluted ammonia and butyric acid served as conditional odor cues (CSs); inhalation of 20% CO2-enriched as US. The US was presented 10 s after CS+ onset and both stimuli co-terminated 30 s later. Subjective anxiety and US-expectancy were measured online upon presentation of the CSs. Respiratory behavior showed a biphasic pattern during CS+ acquisition trials. Participants paradoxically lowered their ventilation first; an increased ventilation was observed only towards the end of the trial. Extinction of this breathing inhibition was found. Participants avoiding the CO2 during acquisition did not show a reduction in fear from acquisition to extinction, whereas non-avoiders did. We conclude that paradoxical decreases in ventilation constitute a relevant behavioral index of fear in CO2-inhalation paradigms.