Background: While the prevalence of malpractice dispute reporting has been decreasing in Taiwan, the gravity of their consequences has been increasing with physicians being increasingly likely to meet litigation, both civilly and criminally, as well as to pay out ever larger settlements. Previous studies have investigated the prevalence of medical malpractice litigation cases in the past few decades; however, no study has focused on the incidence of medical malpractice disputes in Taiwan. Objectives: The purpose of this study was to explore the incidence of medical disputes in Taiwan and to describe the proportion of criminal to civil litigation in medical disputes in Taiwan. Methods: In this study we extracted the number of confirmed malpractice disputes classified as criminal or civil occurring in Taiwan between 1987 and 2012 from the National Medical Dispute Database (NMDD). The specialty-specific incidence was calculated by dividing the number of disputes by the number of physicians in that specialty. The ratio of criminal dispute litigation to civil dispute litigation and the ratio of confirmed and possible malpractice disputes to the total number of disputes were also calculated. Results: The three specialties which encountered the most medical disputes were surgery, obstetrics and gynecology, and internal medicine, respectively. The highest ratio (32.0) of criminal versus civil medical litigation occurred in 1987, and then decreased gradually with the ratio remaining under 10 since 1997, and under five since 2005. The peak proportion of confirmed medical negligence verdicts to total medical disputes was 23.3% and occurred in 1996. Conclusion: This study revealed that the three most frequently accused specialties were surgery, obstetrics and gynecology, and internal medicine in Taiwan. Although no consistent trend was found, there were change points during the period of analysis. The criminal to civil medical litigation ratio showed decreases during the research period. The decreased criminal to civil medical litigation ratio may imply that physicians will be forced to accept the out-of-court settlements due to legal or press pressure.