Introduction Cotrimoxazole preventive therapy (CPT) is a feasible, inexpensive, and well-tolerated way for patients living with HIV/AIDS to reduce HIV/AIDS-related morbidities. The aim of this study was to evaluate the use of cotrimoxazole as a prophylaxis therapy among patients living with HIV/AIDS at Gondar University Referral Hospital (GURH), northwestern Ethiopia.

Methods A retrospective cross-sectional study was conducted at GURH, from September 2013 to October 2015. Medical records of 264 patients were selected by using systematic random sampling technique. Data were collected using the structured checklist and evaluated against World Health Organisation (WHO) guidelines. The quantitative data were analysed using the statistical packages for social sciences Version 20. Descriptive and binary logistic regressio were used to assess the association between different variables.

Results Approximately 95 (36.0%) patients were at WHO clinical stage III at the start of CPT. The use of CPT was consistent with the guidelines in the rationale for indication 200 (75.75%) and dose 263 (99.62%), despite the presence of contraindications in 24 (9.90%) patients. The occurrence of cotrimoxazole-associated side effects was higher in the first month of therapy.

Conclusion Although the practice of discontinuation of CPT and follow-up for adverse drug effects were not consistent with WHO guidelines on the rational use of cotrimoxazole prophylaxis, the use of CPT among people living with HIV/AIDS at GURH was appropriate. Health professionals should adhere to the available updated guidelines to reduce the occurrence of adverse effects.