Background: Structural research on the construct of affect intolerance (an overarching latent construct indicated by distress tolerance and anxiety sensitivity) has only been conducted in adults. Given that a self-report measure of distress tolerance was recently validated for youth and affect intolerance may be a core mechanism of transdiagnostic interventions for internalizing disorders, we examined how affect intolerance relates to internalizing symptoms in youth. We predicted that a latent affect intolerance factor (indicated by distress tolerance and anxiety sensitivity) would be associated with self and parent-reports of youth anxiety, depressive, and obsessive-compulsive symptoms, controlling for age and gender. Methods: At a pre-treatment evaluation, youth with a primary depressive, anxiety, or obsessive-compulsive spectrum disorder (N=277) aged 8-17, and their parent, completed questionnaires. Results: Greater levels of the affect intolerance factor predicted greater youth- and parent-reported youth anxiety, depression, and obsessive-compulsive symptoms, controlling for age. Limitations: Future research should replicate findings in a sample with a greater proportion of depressed youth and utilize experimental or longitudinal methods. Conclusions: Importantly, distress tolerance and anxiety sensitivity are core transdiagnostic processes that can be targeted in cognitive-behavioral interventions. Future research should examine how transdiagnostic interventions for youth with internalizing disorders can target these cross-cutting emotional vulnerabilities.