To date, few studies have been conducted to pairwise compare the prognosis of peritoneal dialysis (PD), unplanned PD, and unplanned hemodialysis (HD). We analyzed longitudinal data from Taiwan's National Health Insurance Research Database. We included 45,165 patients whose initial dialytic modality was PD or unplanned HD between January 1, 2001 and December 31, 2013. We divided the patients into three groups according to their initial dialytic modalities. The primary outcomes were all-cause mortality and death from infection during 1-year follow up. The risks of all-cause mortality and infection death were higher in the unplanned PD group than in the planned PD group (hazard ratio [HR] 1.43, 95% confidence interval [CI] 1.28-1.60; HR 1.54, 95% CI 1.32-1.80). Likewise, the risks of all-cause mortality and infection death were higher in the unplanned HD group (HR 1.64, 95% CI 1.48-1.82; HR 1.85, 95% CI 1.61-2.13). Furthermore, the risks of all-cause mortality and infection death were also higher in the unplanned HD group than in the unplanned PD group (HR 1.15, 95% CI 1.07-1.23; HR 1.20, 95% CI 1.09-1.32). In conclusion, our study demonstrates that patients whose initial modality was planned PD or unplanned PD may have better clinical outcomes than those whose initial modality was unplanned HD.