Background: Several theoretical perspectives suggest that emotion dysregulation is a predisposing risk factor for many psychiatric disorders. Yet despite a rapidly evolving literature, difficulties with emotion regulation (ER) are often measured inconsistently across studies, with little regard to whether different approaches capture the same construct. In this study, we evaluate the correspondence between two widely used measures of emotion dysregulation that cut across self-report and physiological levels of analysis. Our objectives were to (1) evaluate whether youth self-reports of ER difficulties correspond with physiological measures of emotion dysregulation collected at baseline and during sad emotion induction, and (2) validate the Difficulties in Emotion Regulation Scale (DERS) in a youth sample. Method: We measured emotion dysregulation among a sample of youth with depression, conduct problems, comorbid depression/conduct problems, or no psychiatric condition. Youth were assessed initially at ages 8-12 (Year 1) and followed up at Years 2 and 3. Respiratory sinus arrhythmia (RSA), a widely used physiological index of emotion regulation, was measured across all three years during sad emotion induction. At Year 3, the DERS was also administered. Results: Multilevel modeling analyses indicated that slopes in RSA collected across the three assessments were associated with later self-reported ER abilities at the transition into adolescence. These findings were replicated across contexts (baseline and emotional challenge), suggesting that adolescents whose physiological responding to emotional challenge improves also experience fewer difficulties with emotion regulation as they mature.