Objective: Some critics of treatment manuals have argued that their use may undermine the quality of the client-therapist alliance. This notion was tested in the context of youth psychotherapy delivered by therapists in community clinics. Method: Seventy-six clinically referred youths (57% female, age 8-15 years, 34% Caucasian) were randomly assigned to receive nonmanualized usual care or manual-guided treatment to address anxiety or depressive disorders. Treatment was provided in community clinics by clinic therapists randomly assigned to treatment condition. Youth-therapist alliance was measured with the Therapy Process Observational Coding System-Alliance (TPOCS-A) scale at 4 points throughout treatment and with the youth report Therapeutic Alliance Scale for Children (TASC) at the end of treatment. Results: Youths who received manual-guided treatment had significantly higher observer-rated alliance than usual care youths early in treatment; the 2 groups converged over time, and mean observer-rated alliance did not differ by condition. Similarly, the manual-guided and usual care groups did not differ on youth report of alliance. Conclusions: Our findings did not support the contention that using manuals to guide treatment harms the youth-therapist alliance. In fact, use of manuals was related to a stronger alliance in the early phase of treatment. (Contains 3 tables, 1 figure and 3 footnotes.)