In patients with polycystic kidney disease, nephrectomy of native kidneys are often performed at the time of kidney transplantation. We aimed to examine how the extent of nephrectomy affects operation-related outcomes. This was a retrospective study from a single center experience of Inje University Busan Paik Hospital from Jan 2007 to Jan 2019. Among 24 patients with polycystic kidney disease who underwent kidney transplantation, 3 patients had simultaneous single nephrectomy (Group 1), 19 patients bilateral nephrectomy (Group 2), and 2 patients remained with their native kidneys (Group 0). We compared their characteristics and perioperative outcomes. Patients were 50.1±7.4 years old, and 62.5% were men. The baseline characteristics of patients were not different among 3 groups. Operation time tended to increase according to numbers of nephrectomy; 125±0 minutes in Group 0, 258±38 minutes in Group 1, and 322±69 minutes in Group 2 (p=0.002). Although intraoperative blood loss was greater in Group 2 (1242±521 mL) compared to Group 0 (550±354 mL) and Group 1 (417±338 mL) (p=0.02), hemoglobin levels of postoperative day 1 were not different (Group 0, 9.4±0.4 g/dL vs. Group 1, 9.1±0.7 g/dL vs. Group 2, 9.5±1.0 g/dL, p=0.804). Duration from operation to discharge seemed to increase with number of nephrectomy (Group0, 13±4 days; Group 1, 21±5 days; Group 2, 24±9 days), but it was not statistically significant (p=0.225). Delayed graft function occurred in 2 patients from Group 2. Estimated glomerular filtration rate after 1 month of transplantation was not different among 3 groups (72.9±12.9, 51.5±14.0, and 62.8±24.0 ml/min/1.73m2 for Group 0, 1, and 2, p=0.583). The number of native kidney resected simultaneously at the time of kidney transplantation was related to prolonged operation and increased bleeding during operation, though it did not adversely affected short-term post-operative outcomes.