This study examined the relationship of negative affect and alcohol use behaviors to baseline respiration and respiratory response to emotional challenge in young adults (N = 138, 48 % women). Thoracic-to-abdominal ratio, respiratory frequency and variability, and minute volume ventilation were measured during a low-demand baseline task, and emotional challenge (viewing emotionally-valenced, emotionally-neutral, and alcohol-related pictures). Negative mood and alcohol problems principal components were generated from self-report measures of negative affect and mood, alcohol use, and use-related problems. The negative mood component was positively related to a thoracic bias when measured throughout the study (including baseline and picture exposure). There was generally greater respiratory activity in response to the picture cues, although not specifically in response to the content (emotional or alcohol-related) of the picture cues. The alcohol problems component was positively associated with respiratory reactivity to picture cues, when baseline breathing patterns were controlled. Self-report arousal data indicated that higher levels of negative mood, but not alcohol problems, were associated with greater arousal ratings overall. However, those with alcohol problems reported greater arousal to alcohol cues, compared to emotionally neutral cues. These results are consistent with theories relating negative affect and mood to breathing patterns as well as the relationship between alcohol problems and negative emotions, suggesting that the use of respiratory interventions may hold promise for treating problems involving negative affect and mood, as well as drinking problems.