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*Objective*: Juveniles under community supervision have a higher prevalence of substance use compared to the general population. Previous research has examined factors that predict treatment outcomes once treatment has been initiated; however, there is a gap in the literature regarding the factors that affect initiation of treatment, particularly after referral by the juvenile justice system. This study analyzes individual-level factors with site and state-level variation predicting initiation of treatment following referral from juvenile probation agencies. *Methods*: Using the Behavioral Health Services Cascade framework of the Juvenile Justice-Translational Research on Interventions for Adolescents in the Legal System (JJ-TRIALS) multisite project, a series of mixed effects logistic regression models were estimated using two methods. Referral and treatment initiation data from two analytic methods addressing missing data from 3,312 youth records in Method 1 and 5,325 records in Method 2 collected from 22 counties across six states were analyzed. We examined between site variation and assessed the impacts of individual- and state-level factors on initiation to treatment after referral. *Results*: Results from the mixed effects model indicate that being referred and initiating treatment varied significantly across sites in both Methods. A mixed model in Method 1 with individual-level characteristics indicated that youth with a higher substance use treatment need and youth with a higher supervision level are 1.98 and 1.74 times more likely to initiate treatment after referral, respectively. In Model 3 for Method 2 analyses, when controlling for state-level differences, youth with a higher level of supervision were 2.26 times more likely to initiate treatment following referral compared to those with a lower level. *Conclusion*: Findings suggest that individual factors matter in predicting initiation, independent of state or site. Level of supervision is the most salient factor in a youth’s initiate of treatment in both missing data methods, however, need for treatment is also important although it was significant in Method 1 only. Understanding the differences in predictors allows partnering behavioral health and juvenile justice agencies to develop strategies to increase the likelihood that referred youth initiate treatment.
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