Using cluster analysis techniques, we identified two distinct clusters of newly homeless adolescents in Los Angeles (n = 261): those who are protected and doing relatively well while out of home with more protective than risk factors, and those who are risky with more risk than protective factors. The objective of this study was to examine the trajectories of human immunodeficiency virus (HIV) risk behaviors and exiting homelessness among protected newly homeless adolescents, compared to those who are classified as risky. HIV risk behavior included unprotected sex, having multiple sex partners and hard drug use. Logistic regression mixed-effects models were used to evaluate the trajectories of HIV risk behaviors and exiting homelessness over time. The adolescents in the protected group reported significantly less unprotected sex ( p = 0.0156), being abstinent or monogamous ( p < 0.0001) and less hard drug use ( p < 0.0001) compared to the adolescents in the risky group. In addition, the protected group reported more "exiting homelessness", compared to the risky group ( p = 0.0007). However, the differences in the level of unprotected sex between the protected and risky groups decreased over time. Our findings confirm the notion that newly homeless adolescents are indeed heterogeneous. Given that the risk behavior profiles of protected group merges to the risky group over time, our findings underscore the need to mount tailored interventions to be designed for the protected group early in the process.