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Readiness to change constitutes an important treatment target. This study examined white matter (WM) integrity as a possible link in the pathway between motivation to abstain and treatment outcome. Adolescents (age 14–18 years, n = 32) were recruited from intensive outpatient (IOP) substance use treatment and reported on motivation to abstain from alcohol and marijuana shortly after treatment admission (i.e., at baseline). Diffusion tensor imaging data were collected approximately 7 weeks after starting IOP and were used to quantify WM integrity (indexed by fractional anisotropy, FA) using a region of interest (ROI) approach. Treatment outcomes were assessed 6 months after baseline. Indirect effects analyses tested FA in prefrontal, orbitofrontal, and temporal ROIs as a linking variable in the pathway from motivation to abstain to alcohol and marijuana outcomes. Bivariate correlations indicated that greater motivation to abstain from alcohol was associated with lower FA in prefrontal, orbitofrontal, and temporal ROIs and that lower FA in these three ROIs was associated with greater 6-month alcohol problem severity. The indirect effect of FA was significant for the prefrontal ROI in the pathway from motivation to outcome for alcohol. FA values were not associated with motivation to abstain from marijuana or marijuana-related outcomes. Results suggest that lower WM integrity, particularly in the prefrontal brain region, may help to explain greater alcohol problem severity at 6 months despite higher motivation to abstain from alcohol. Interventions that aim to enhance WM integrity warrant attention to improve adolescent treatment outcomes.