The Juvenile Sex Offender Assessment Protocol-II (J-SOAP-II) is a tool used to aid clinicians in assessing the sexual and criminal reoffense risk of male youths who have committed a sex offense. Despite its popularity, the factor structure has not been thoroughly assessed. The present study used confirmatory factor analysis (CFA) to test the factor structure of the four subscales of the J-SOAP-II in a group of youths aged 12-18 who were confined for sexual offenses (N = 909), and whether the fit is affected by youth race. The results showed a poor fit to the data. An ad-hoc goal was added, to propose a new factor structure using exploratory factor analysis (EFA) on one half of the data, and CFA on the second half of the data. The EFA identified three-factors: Sexual Offending and Victimization History, Risk for General Delinquency, and Antisocial Beliefs and Attitudes. This three-factor model, provided an improved, but not good, fit, indicating that further modifications to the J-SOAP-II are required to meaningfully capture risk-relevant latent constructs.