Although the vast majority of depressed patients visit primary health care clinics, they often remain undiagnosed and untreated. Therefore, early detection in primary care settings is important. There is a high correlation between number of physical symptoms and the presence of depression, yet little has been reported regarding this relationship in Japanese primary care clinics. We examined number of physical symptoms and depression in a department of general medicine of a Japanese hospital. We included patients with unexplained symptoms after multiple tests to rule out organic diseases. Twenty-one common symptoms were assessed using a symptom checklist. Depression was diagnosed using the Patient Health Questionnaire-9, a self-administered questionnaire designed to diagnose depression. Among 386 patients, 105 (27.2%) (average age: 49.7 ± 20.9 years, 28 men and 77 women) met the criteria for depression. Among the 21 symptoms, 14 were significantly more frequent in patients with depression than in those without depression. When patients had neither general fatigue, nor sleep disturbance nor appetite loss, none met the criteria for depression. Number of symptoms was significantly higher in patients with compared with those without depression. The prevalence of depression increased with number of symptoms: 2% (2/100) for 0 or 1 symptom, 42.4% (42/99) for four to five symptoms and 68.7% (22/32) for more than nine symptoms. Japanese primary care physicians can often rule out depression when patients have neither general fatigue, nor sleep disturbance nor appetite loss. A diagnosis of depression should be considered in patients who report multiple physical symptoms.