BACKGROUND: Sexually transmitted infections (STIs) are a public health problem in Vietnam with sub-optimal care in medical practice. Identifying practitioners' perceived barriers to STI care is important to improve care for patients with STIs. METHODS: A cross-sectional survey was conducted among 451 physicians. These physicians were dermatology and venereology (D&V) doctors, obstetrical/gynaecological (Ob/Gyn) doctors, general practitioners, and assistant doctors working in health facilities at provincial, district and communal levels in three provinces in Vietnam. RESULTS: Almost all (99%) respondents mentioned at least one barrier to STI care. The barriers were "lack of STI training" (57%), "lack of professional resources" (41%), "lack of time" (38%), "lack of reimbursement" (21%), "lack of privacy/confidentiality" (17%), "lack of counselling" (15%), and "not the role of primary care provider" (7%). Multivariable logistic regression analysis showed that "lack of professional resources" was associated with respondents being in medical practice for ten years or under (vs. 11-20 years), and working at district or communal health facilities (vs. provincial facilities); "lack of time" were associated with respondents being female, seeing more than 30 patients a week (vs. <15 patients/week); and "lack of privacy/confidentiality" was associated with physicians' seeing more than 30 patients a week (vs. <15 patients/week). CONCLUSION: The study has identified several barriers to STI care in medical practice in Vietnam. Results of the study can be used to improve areas in STI care including policy and practice implications.