Pemphigus is a potentially life-threatening autoimmune blistering disease. However, little is known about the all-cause and cause-specific mortality among patients with pemphigus compared with the general population. The incidence of pemphigus in Taiwan has not been described previously. The objective of this study was to estimate the incidence of pemphigus in Taiwan and to investigate the overall mortality, causes of death, and cause-specific mortality in a nationwide population-based cohort of pemphigus patients. The study cohort included 853 patients newly diagnosed with pemphigus between 2002 and 2009 in the National Health Insurance Research Database. Survival status, date of death, and cause of death were ascertained by linking the study cohort with the National Register of Deaths Database of Taiwan. All-cause and cause-specific standardized mortality ratios (SMRs) were estimated. The incidence of pemphigus in Taiwan was 4.7 (95% confidence interval (CI), 3.2-6.2) per million per year. Overall, 88 deaths were observed during a mean follow-up period of 3.8 years, which was more than two times the number expected (SMR, 2.36; 95% confidence interval, 1.92-2.91). In the analysis of causes of death, the SMRs for death due to pneumonia (3.64; 95% CI, 1.30-10.21), septicemia (11.57; 95% CI, 2.95-45.34), cardiovascular disease (2.69; 95% CI, 1.18-6.12), and peptic ulcer disease (8.44; 95% CI, 1.22-58.21) were significantly higher than expected. We concluded that the incidence of pemphigus is not low in Taiwan, and the overall mortality among pemphigus patients is two times greater than that of the general population. In particular, patients with pemphigus have higher risk of mortality from systemic and respiratory tract infections, cardiovascular disease, and peptic ulcer disease.