Abstract Background Despite recent reductions, youth substance use continues to be a concern in the United States. Structured primary care substance use screening among adolescents is recommended, but not widely implemented. The purpose of this study was to describe the distribution and characteristics of adolescent substance use screening in outpatient clinics in a large academic medical center and assess related factors (i.e., patient age, race/ethnicity, gender, and insurance type) to inform and improve the quality of substance use screening in practice. Methods We abstracted a random sample of 127 records of patients aged 12–17 and coded clinical notes (e.g., converted open-ended notes to discrete values) to describe screening cases and related characteristics (e.g., which substances screened, how screened). We then analyzed descriptive patterns within the data to calculate screening rates, characteristics of screening, and used multiple logistic regression to identify related factors. Results Among 127 records, rates of screening by providers were 72% (each) for common substances (alcohol, marijuana, tobacco). The primary method of screening was use of clinical mnemonic cues rather than standardized screening tools. A total of 6% of patients reported substance use during screening. Older age and racial/ethnic minority status were associated with provider screening in multiple logistic regression models. Conclusions Despite recommendations, low rates of structured screening in primary care persist. Failure to use a standardized screening tool may contribute to low screening rates and biased screening. These findings may be used to inform implementation of standardized and structured screening in the clinical environment. Clinical trial registration not applicable.