INTRODUCTION This systematic review aimed to synthesize existing studies on stigma (patient or provider's perspective) related to screening, brief intervention, and referral (SBIR) for tobacco use, alcohol use, and insufficient physical activity. METHODS We conducted a systematic review in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). We systematically searched articles in MEDLINE, CINAHL, EMBASE, and Web of Science databases using predetermined keywords. We reviewed both the title/abstract and full text using an a priori set of inclusion and exclusion criteria to identify the eligible studies. We appraised study quality, extracted data, and summarized the characteristics of intervention design and study findings from the included studies. RESULTS No published studies were found pertaining to SBIR related to stigma for tobacco use or insufficient physical activity. Five studies were included in the review; all focused on SBIR-related stigma for alcohol use. The studies reported that patients perceive stigma in accessing treatment for alcohol use in healthcare settings. Our review identified that patients who consume alcohol fear being judged or stigmatized by their provider, which may lead patients to provide dishonest answers and hide their alcohol use status. We identified that patients are concerned about the confidentiality of the information collected on alcohol use and its impacts on their employment and housing. CONCLUSIONS Patients' fear of being judged or stigmatized prevents them from getting treatment for alcohol use and reduces providers' ability to engage and support patients. More studies are needed to explore stigma related to SBIR for risk factors (including tobacco use and physical activity) using standardized stigma measurement tools.