Post-transplant diabetes mellitus (PTDM) is a complication which reduces allograft and recipient life-span. Polygenic risk scores (PRS) robustly show association with greater type 2 diabetes (T2D) development risk. We examined T2D-PRS in transplant recipients and donors using genome-wide genotyping in 1581 liver recipients, and 1555 donors and 2062 kidney recipients and 533 donors from four centers. Liver and kidney recipient T2D-PRS was associated with pre-transplant T2D and PTDM development. Liver donor, but not kidney donor, T2D-PRS was an independent risk factor for PTDM development. Inclusion of a combined liver recipient and donor T2D-PRS significantly improved PTDM prediction vs clinical characteristics-only models: AUC (95%CI): 67.6% (64.1% − 71.1%) vs. 62.3% (58.8% − 65.8%), p = 0.0001. Liver recipients in the highest quintile of recipient-donor combined T2D-PRS had the greatest PTDM risk: OR (95%CI) = 3.22 (2.07–5.00), p = 1.92E-07, compared to the lowest quintile. T2D-PRS allows identification of transplant candidates with high PTDM risk, for whom early preemptive diabetes management is warranted. Pre-transplant knowledge of donor T2D-PRS in the setting of living liver donation should optimized selection of donors to reduce PTDM.