Basic medical sciences play an important role in developing students’ knowledge and preparing them for clinical practice; however, their alignment with the actual needs of general medical practice remains a matter of debate. This study aimed to evaluate the alignment of the basic sciences phase with the clinical needs of general medicine from the perspectives of students and recent graduates at Mashhad University of Medical Sciences.

This descriptive-analytical cross-sectional study was conducted from August 2024 to August 2025. A total of 601 students at the end of the basic sciences and internship phases and recent general medicine graduates participated through census sampling. Data were collected using the basic sciences section of a comprehensive questionnaire for evaluating the general medical education program. The questionnaire was developed based on the American Association of Medical Colleges (AAMC) Graduation Questionnaire and informed by 75 semi-structured interviews with graduates, with adaptations to the context of Mashhad University of Medical Sciences. This section assessed the alignment of course content, course volume, practical training, and scientific foundations of basic sciences with clinical needs. Content validity was evaluated by 10 faculty members (CVR = 0.65, CVI = 0.78), and reliability was confirmed using Cronbach’s alpha (α = 0.7). Data were analyzed using SPSS version 26, Pearson’s chi-square, and Fisher’s exact tests.

The results showed heterogeneous alignment between course content and clinical needs. Physiology, parasitology and mycology, pharmacology, pathology, and microbiology showed the highest alignment (>50%), whereas biochemistry, medical physics, genetics, medical statistics, and histology showed the lowest. The volume of many courses, particularly biochemistry (77%), anatomy, and medical physics, was perceived as excessive. Evaluations of practical training varied, with a considerable proportion of participants considering it adequate. Approximately 70% of respondents rated the alignment of basic sciences foundations with clinical skills as weak or very weak in physical examinations, common complaints/diseases, and interpretation of laboratory tests and preclinical images. Only about half of the participants rated the adequacy of developing an overall understanding of the structure and function of the human body as favorable. Significant differences according to demographic variables were scattered and showed no consistent pattern.

The findings indicate a perceived gap between basic sciences education and its clinical application. Curriculum revision emphasizing horizontal and vertical integration, prioritization of content based on clinical needs, problem- and clinical scenario-based learning, and earlier clinical exposure may help reduce this gap and enhance professional readiness. The self-reported nature of the data and single-center design limit generalizability.