Background Few studies have explored factors affecting preference of medical students towards general practice as a career choice. We conducted a survey in Karachi across various public and private sector medical colleges to examine factors associated with students' general practice career aspirations in Karachi, Pakistan. Methods From January to March 2018, we distributed a 21-item questionnaire to final year medical students in eight medical schools. The survey asked students about their top three career preferences from 19 specialty fields, their demographics and their career priorities. Multivariable logistic regression was used to determine the effect of each item. Results A total of 1400 responses were obtained. The top five specialty fields chosen by students with their numbers were: internal medicine, 898 (64.2%); general practice, 337 (24.1%); pediatrics, 449 (32.1%); surgery, 380 (27.2%); and emergency medicine, 243 (17.4%). The "intent to inherit existing practice" and "other academic or professional experiences prior to medical school" had a positive association with choosing general practice while "having a physician parent'' had a negative association among the medical students demographics after adjusting for other covariates in the multivariable logistic regression. Medical students who ranked "clinical diagnostic reasoning", "community-oriented practice", "involvement in preventive medicine", and "frequent patient communication" as highly important were more likely to choose general practice, whereas, "access to advanced medical fields", "mastering advanced procedures", and "depth rather than breadth of practice" were less likely to be associated with general practice aspiration. Conclusion The study's results depicted limited interest of family medicine as a career option in graduating students, and pointed out the factors that likely influence the choice of general practice as a career are clinical diagnostic reasoning, community-oriented practice and preventive medicine.