Background Contrast-enhanced ultrasound (CEUS) and power Doppler ultrasound (US) are established tools in the study of acute renal allograft (RA) dysfunction. The aim of this study was to investigate their long-term prognostic impact. Materials and Methods A total of 39 kidney recipients underwent CEUS and US at 5 and 15 days and at 1, 3, 6, and 12 months after grafting, with yearly clinical, laboratory, and US follow-up for a total of 4 years. CEUS analysis according to the gamma variate model was performed on cortical and medullary regions. Patients were divided into 2 subsets: death or graft failure vs patients with functioning grafts; higher vs lower than 50% glomerular filtration rate (GFR) reduction from the first month to the fourth year after grafting. Receiver-operator characteristic (ROC) analysis for death/graft failure and 50% GFR reduction events was performed for variables with significant differences between groups (t test) or with significant correlation to GFR (Pearson correlation). Results ROC analysis confirms the reliability of clinical and radiologic variables for the evaluation of long-term graft survival or of GFR reduction, with high sensitivity (for resistive index) or specificity (for GFR, medullary peak, and regional blood flow). Conclusions Combining CEUS and US allows the evaluation of long-term RA function in terms of GFR reduction and graft survival. Resisitive-indexes show a good sensitivity, relating to kidney disfunction, while CEUS parameters show a good specificity, identifiying well-perfused grafts.