Background Pre-exposure prophylaxis (PrEP) for individuals at significant risk for Human Immunodeficiency Virus acquisition is approved for individuals weighing at least 35 kg by the Food and Drug Administration. This cross-sectional study analyzed indications for PrEP in a clinical setting. Methods There were 429 charts reviewed from adolescents between 15 and 21 years old seen for preventive care visits at an adolescent primary care center in the Deep South during a 1-year timeframe. Univariate and multivariable regression analyses were completed to identify factors associated with indications for PrEP. Results Forty-four percent of 429 adolescents (between 15 and 21 years) had a PrEP indication; 77% were women and 95% heterosexual. Significant factors associated with an indication for PrEP included living with a nonparent or nonrelative and polysubstance use. No adolescents with an indication for PrEP were prescribed PrEP. A sensitivity analysis comparing indications for PrEP between the 2014 and 2017 The Centers for Disease Control and Prevention Guidelines revealed no significant differences in percent with an indication (44.5% vs. 42.8%) or factors associated with indications. Conclusions Pre-exposure prophylaxis as a biomedical tool for adolescents and young adults (AYAs) may remain underutilized. A key factor in improving utilization involves providers being able to recognize AYAs who may have an indication for PrEP with a specific focus on those AYAs who do not live in households with parents or a surrogate family member and those who are polysubstance users.