Our previous study revealed over 50% of recipients with pre-transplant impaired glucose tolerance (IGT) improved to normal glucose tolerance after kidney transplantation. However, the mechanism is unclear. We aimed to investigate whether the changes in glucose tolerance are associated with beta-cell function and insulin resistance in Japanese kidney transplant recipients with pre-transplant IGT. Of the 265 recipients who received kidney transplantation, 54 with pre-transplant IGT were included. We divided the recipients into improvement and non-improvement groups according to the change in the area under the curve for glucose obtained from the oral glucose tolerance test (OGTT). Beta-cell function was estimated by the insulin secretion sensitivity index-2 (ISSI-2) and the disposition index (DI). Insulin resistance was estimated by the Matsuda index (MI) and the homeostasis model assessment of insulin resistance (HOMA-IR). ISSI-2, DI increased significantly after transplantation in the improved group ( P<0.01, P<0.05, respectively), but not in the non-improved group. ΔISSI-2 and ΔDI were significantly and positively associated with pre-transplant 60-minute OGTT plasma glucose levels (both P<0.01). There were no differences in MI or HOMA-IR between these two groups after transplantation. In recipients not on pre-transplant dialysis, a significant negative association was found between Δblood urea nitrogen (BUN) and ΔDI (correlation coefficient: −0.48, P<0.05). In pre-transplant IGT recipients, improvements in glucose tolerance after kidney transplantation were linked to improvements in beta-cell function. The higher the 60-minute OGTT plasma glucose level, the greater the improvement in post-transplant beta-cell function. Improvements in BUN after transplantation were associated with improvements in beta-cell function.