Background No previous research has targeted educators regarding educational practice and the achievements of students in terms of the learning objectives of clinical clerkships in university general medicine departments of Japan. We aimed to clarify the characteristics of clinical clerkships in Japanese general medicine departments using a questionnaire administered to chairpersons of university general medicine departments. Methods This was a descriptive questionnaire-based study using Google Forms (Google, Inc., Mountain View, CA, USA). We asked the chairpersons of general medicine departments in Japanese universities the following questions, with responses given on a 5-point Likert scale: Question 1: How well are primary symptoms in the national model core curriculum for undergraduate medical education taught in clinical clerkships in university general medicine departments? Question 2: How successfully can students achieve the learning objectives of the national model core curriculum for undergraduate medical education through clinical clerkships in general medicine departments of university hospitals? Question 3: How successfully can students achieve the learning objectives of the national model core curriculum for undergraduate medical education through clinical clerkships in other community clinics or hospitals?The results of the questionnaire responses are described as mean±standard deviation. Results Of the 71 Japanese universities with general medicine departments, 43 were included in the analysis. For Question 1, the symptoms and pathophysiologies with a mean score of 4 points or higher were fever, general malaise, anorexia, weight loss or gain, edema, abdominal pain, lymphadenopathy, and headache. All those symptoms require basic medical competencies. For Questions 2 and 3, the intramural clinical clerkship of general medicine departments had a higher mean score than the extramural clinical clerkship for diagnostic reasoning that emphasizes medical history and physical examination and a comprehensive approach to patients with multiple health problems.In contrast, the extramural clinical clerkship, in which medical students can build experience with community-integrated care, had a mean score of 3 points or higher for all items. Conclusions The clinical clerkship in general medicine departments of Japanese universities provides students with chances to acquire clinical competencies regarding primary symptoms and pathophysiologies. Additionally, the extramural clinical clerkship provides experience in community-based integrated care, including home medical care, collaboration, health and welfare, and long-term care.