Objective: To determine the frequency of suicidal ideation, its risk factors and clinical manifestation in Pakistani medical students. Methodology: This cross sectional study was carried out through a self-made questionnaire having 22 items which was administered among medical students of eight colleges, all over Pakistan. Students were selected through consecutive non-probability sampling. The data were analyzed by SPSS version 21. Results: Out of the total sample size of 1132, 47.9% were male and 52.1% were female. Out of total, 49.2% were in pre-clinical year (1st and 2nd year) and 50.8% were in clinical years (3', 4th and 5th year). About 6.8% of the medical student had suicidal ideation and 9.5% had the desire to harm themselves. Majority (82.7%) choose medical profession by their will; 62.5% were found out to be fully satisfied by their medical college. Effects of stress like irritability, inability to sleep, fatigue, depression, decrease appetite, headache, feeling of anger, desire to harm oneself, fainting spells/ dizziness/ blackouts, feeling of being unworthy, thoughts of leaving medical education, fighting with others were found to be significantly (p< 0.05) associated with suicidal thoughts. Conclusion: A significant percentage of medical students were found to have suicidal ideation. Medical students who joined medical colleges without their free will or whose parents were unable to afford medical education or students with significant past or family history of depression and anxiety or significant health problem or poor interaction with their family members had a significantly greater risk of suicidal ideation.