Acquired renal cystic disease develops in the native kidneys of patients with renal allografts with longstanding poor function. However, there has been no long-term prospective study of the regression or development of cysts in native kidneys of renal allograft recipients with good long-term function (serum creatinine: 114 ± 24 µmol/l). We followed 61 renal allograft recipients for 63.5 ± 29.0 months (mean ± SD) using computed tomography (CT scan) every 1 or 2 years after transplantation. The cyst grade at pretransplantation was significantly reduced at the first study after transplantation (0.98 ± 1.39 vs. 0.57 ± 0.96; p < 0.01). Baseline study after transplantation revealed that the incidence of cysts in native kidneys was 22/61 (36.1 %) and 26/61 (42.6%) in the follow-up study. In 32 patients (52.5%), there were no visible cysts in the native kidneys. In 9 patients (14.8%), there was no change in the number of cysts during follow-up, while in another 9 patients the number of cysts decreased. On the other hand, the number of cysts increased in 11 patients (18.0%) during follow-up. The mean follow-up duration was longer in the group with an increased number of cysts than in the groups with no visible cysts or a decrease in number. Biochemical analysis of cyst fluid from newly developed cysts in 2 patients showed differences from the pattern in acquired renal cystic disease of hemodialysis patients. These results indicate that after regression of acquired cysts in most allograft recipients, no or only a few cysts persist in patients with good graft function. The remaining cysts continue to regress further in some patients. On the other hand, the development of new cysts occurs in the native kidneys of some patients (18 %). These newly developed cysts may be different in nature from those of acquired renal cystic disease in hemodialysis patients.