Because Pneumocystis jirovecii pneumonia (PJP) is a serious infection in immunocompromised patients, several guidelines recommend PJP prophylaxis after renal transplantation. But, there is a concern related to drug toxicity and various PJP incidence by regional groups. By comparing two groups in single hospital that is divided by PJP prophylaxis from two different physician's preference, we analyzed the effect of PJP prophylaxis on actual PJP incidence by period after renal transplantation. We conducted a retrospective analysis of 578 patients who received renal transplantation at Seoul National University Hospital between January 2011 and December 2015. We used low dose Trimethoprim/sulfamethoxazole (TMP-SMX) for PJP prophylaxis (PO 480mg daily) within 1 month after renal transplantation and continued until 6 months. Premature interruption of low dose TMP-SMX was shown in 70 patients (29%) among the group with PJP prophylaxis (n = 241) and major cause (80%) was nephrotoxicity. Mean medication period of them was 65.329 days and we considered that they did not have PJP prophylaxis. No statistically significant differences was shown between two groups regarding donor origin (living or deceased), donor relationship, re-transplantation, HLA mismatch (>3), basal immunosuppressive agent regimen & level, and number of anti-rejection treatment. We divided subgroups into ‘high risk group’ and ‘low risk group’ depending on the preoperative desensitization and ATG induction. PJP incidence after renal transplantation was significantly low in high risk group with PJP prophylaxis, especially in first 6 months. (p = 0.003) However, in the low risk group, 5 (3.9%) of the 127 patients with PJP prophylaxis and 22 (6.3%) of the 337 patients without PJP prophylaxis were diagnosed with PJP in total follow up period. (p = 0.330). And there was also no significant difference in the first year after surgery.  (p = 0.191) Although PJP did not occur during the 6-month prophylaxis period, it did not affect the occurrence of PJP after that time. Therefore, we are questioning how long we have to maintain low dose TMP-SMX prophylaxis after surgery despite the risk of side effects of drug. Our data suggests the selective prophylaxis for high risk group and further research to find other risk factors for PJP after renal transplantation is needed. And we need to think about adjusting the dosage of drug for Koreans.