The goal of this study is to explore providers' patterns of implementation by investigating how community mental health providers selected therapy practice modules from a flexible, modular evidence-based treatment working with youths with comorbid mental health problems. Data were obtained from 57 youths, 5-15 years old, presenting with anxiety, depressive, and/or conduct problems and their 27 providers during their participation in an effectiveness trial involving a modular evidence-based treatment. Although all youths evidenced clinically elevated symptomatology in at least two problem areas, providers targeted youths' comorbid problems with only about half of their study cases. Practice modules indicated for youths' comorbid problems were typically used less frequently and with less depth relative to practice modules indicated for youths' principal clinical problem and were often transdiagnostic in nature (i.e., designed to target more than one problem area). To determine whether providers' decisions to target youths' comorbid problems were systematic, multilevel, logistic regression analyses were conducted and revealed that youths' pretreatment characteristics and time in therapy influenced providers' patterns of module selection. Providers tend to use, but not exploit, the flexibility allowed by modular EBTs and to focus treatment on youths' principal presenting problem. In addition, providers appear to make these practice choices in a systematic and rational manner, and whether and which choices are associated with improved outcomes is an important area of future study.