Objective Based on the cases collected in eight hospitals in Shanghai in recent three years, causes of medical disputes in Shanghai and influence factors of medical dispute levels were discussed, and targeted suggestions were put forward. Methods Multistage sampling were used to collect 561 cases of medical disputes occurred in two Class A Tertiary hospitals, two Class A Secondary hospitals and four community hospitals in Shanghai in recent three years. On the basis of questionnaire, the causes of medical disputes were analyzed by descriptive statistics and the factors affecting the level of medical dispute were analyzed by means of one-way ANOVA and Logistic regression analysis.Results Factors of doctor and patient are involved in the causes of medical disputes, with 87.1% disputes related to doctors and 13.9% related to patients. The doctor’s factors include lack of communication (28.82%), low technical level (16.91%), lack of sense of responsibility (8.86%), defective case records (6.92%), imperfect operation (6.44%), inadequate experience (6.44%), inadequate condition evaluation (5.8%), irregular management process (4.03%), violation of diagnosis and treatment regulation (4.03%), misdiagnosis and mistreatment (3.54%), belated diagnosis and treatment (2.58%), postoperative complications (2.42%), equipment problems (1.13%), missed diagnosis (0.81%), poor condition monitoring (0.48%), unreasonable charge (0.48%) and poor service attitude (0.32%). The patient's factors include misunderstanding of medical behavior (43.48%), high expectation of prognosis (25%), bad attitude (13.04%), inadequate medical knowledge (7.61%), disturbance (6.52%), poor compliance (3.62%) and mistrust (1.09%). Among all medical disputes, there are 406 cases of level-4 medical disputes (78%), 95 cases of level-3 medical disputes (18%), 19 cases of level-2 medical disputes (4%), and no level-1 medical dispute. Meanwhile, the classification of diseases, treatment effect, doctors' violation of diagnosis and treatment regulation, and low technical level are the reasons for the level differences in medical disputes.Conclusion Factors of doctor in medical disputes in Shanghai mainly include inadequate communication and low technical level while the patient’s factors mainly contain misunderstanding of medical behavior and high expectation of the prognosis. Level-3 and 4 medical disputes take up the major part in all medical disputes. The classification of diseases, treatment effect, doctors' violation of diagnosis and treatment regulation, and doctor’s deficient technical level are high-risk factors requiring critical attention in medical disputes.