Abstract Background: Medical malpractice litigation has become an important issue worldwide. Although many epidemiological studies have been carried out, most studies were conducted cross-sectionally in developed countries and focused on malpractice litigation. We conducted nationwide surveys to investigate physicians' experiences associated with malpractice in 1991 and 2005, respectively. Methods: By stratified systemic sampling, questionnaires were mailed to physicians in 1991 and 2005. Physicians were asked about the experience of medical malpractice and outcomes of malpractice. The outcomes of the malpractice were classified as resolution, settlement and lawsuit. We also collected physicians' demographic and professional characteristics. Results: The prevalence of malpractice experience decreased from 44.1% in 1991 to 36.0% in 2005 (P = 0.004). The estimated annual malpractice claims decreased from 0.14 to 0.10 per physician in 1991 and 2005, respectively (P < 0.001). Physicians 45–64 years of age, obstetrician/gynaecologists and surgeons had significantly higher risk of malpractice. Compared with 1991, malpractice claims in 2005 were more likely to be brought into courts (23.1% in 2005 vs 15.7% in 1991, odds ratio (OR) = 1.48, P = 0.020). In litigation cases, malpractice events in 2005 had more than triple the risk of 1991 to be sued in both civil and criminal courts (12.4% in 2005 vs 4.1% in 1991, OR = 3.31, P < 0.001). Conclusion: Compared with 1991, medical malpractice experiences were decreasing in prevalence, but increasing in severity in 2005. Additional studies, especially among different legal systems, are necessary to confirm these observations.