An important aspect of the medical program is the Hospital Clinical Training. The BAUFM has academic affiliation with several hospitals, where undergraduate and postgraduates medical students receive their training.

Hammoud Hospital University Medical Center is a 325-bed facility that treats more than 24,000 patients per year, and performs more than 10,000 surgeries per year. The hospital has one of the biggest Cardiac programs in Lebanon and performs the highest number of renal transplants in the country. It also has an outpatient clinic and handles nearly 100,000+ outpatient visits.

Makassed General Hospital is a 200 patient-bed, which is located in a heavily populated area of Beirut. It is among the top medical facilities in Lebanon and is supported by more than 200 attending and resident physicians and 640 technical and administrative staff. It serves nearly 100,000 in-patients and in excess of 50,000 outpatient visits per year.

Dar al Ajazza al Islamia Hospital, was established in 1952, and has an immense capacity of medical services. The hospital still has a lack of place to meet the great demand which is exposed to. An important part of the training of BAU_FM medical students is to visit and have exposure to patients at Dar Al-Ajaza Al-Islamia Hospital, which is a charitable human institution that offers medical aid.

Saida University Governmental Hospital is a building consisting of four floors that includes Laboratory, Radiology, Lithotripsy, Emergency Departments, in addition to Endoscopy Unit, One Day Surgery (ODS), Stress test nerves and muscles Room and EEG-EMG Room. The hospital also has Obstetrics, Pediatrics, Dialysis, Medical, Surgical, and Intensive Care Departments. The Outpatient Department (OPD) is located in a separate building.

In addition, 3 Primary Healthcare Centers (PHC) are designated as the main teaching sites for students trained in Family Medicine module.