Objective Suicide victims are likely to visit a primary care provider within 1 month of the suicide attempt. However, it is impossible for primary care providers to screen all patients for suicidal ideation or attempts. We, therefore, aimed to investigate potential differences in the chief diagnoses received by primary care patients with and without suicidal ideation, as this information may provide clues and predict patients at risk of suicide. Methods This cross-sectional study included 1,211 Korean adults aged ≥20 years who had participated in the Korea National Health and Nutrition Examination Survey during 2014 and provided information about their histories of suicidal ideation and visits to primary care providers. Multiple logistic regression analyses were used to examine whether suicidal ideation was associated with specific diseases after controlling for age, sex, household income, education, occupation, marital status, smoking, alcohol consumption, and physical activity. Results Among primary care patients, the sample-weighted percentage of suicidal ideation was approximately 12%. The diagnoses of neoplasm and mental disorder were associated with a higher likelihood of suicidal ideation {odds ratio (OR) [95% confidence interval (CI)] 8.32 (1.01–68.56) and 6.19 (1.72–22.33), respectively}. Notably, diseases of the musculoskeletal system and connective tissue were also associated with suicidal ideation [OR (95% CI): 1.93 (1.09–3.43)]. Conclusion The observed visit patterns and correlations of certain diagnoses with suicidal ideation suggest that primary care physicians should pay attention to patients with relevant disorders, consider screening suicidal ideation, and properly consult to a psychiatrist.