This study aimed to identify the parenchymal structural features by both computed tomography (CT) and histology that are associated with death-censored graft failure in recipients of living donor kidneys. We analyzed kidney recipients of ABO-compatible living donor kidneys from 2000-2020 with follow-up through 2023. Cortical volume and thickness, individual medullary pyramid volume and count, glomerular volume, nephrosclerosis, and nephron number were assessed by deep learning models applied to the predonation CT and by morphometric histology analysis from the biopsy at the time of transplantation. There were 3098 recipients followed for a median of 5 years with 346 graft failure events. In adjusted analyses, the only structural measures associated with graft failure were fewer medullary pyramids on CT and a higher fraction of interstitial fibrosis and tubular atrophy on histology. Having ≤15 pyramids donated occurred in 9% and was associated with a graft failure incidence of 2.5 per 100 person-years compared to 1.6 per 100 person-years in the 17% with ≥26 pyramids donated. Fewer medullary pyramids were associated with a lower 1-year estimated glomerular filtration rate, which mediated the subsequent risk of graft failure. Interstitial fibrosis and tubular atrophy >
1% is also associated with graft failure. Medullary pyramid count is a potentially useful predonation prognostic biomarker for graft failure in transplant recipients.