We examined 25 complete and partial nephrectomy specimens from 21 patients with advanced reflux nephropathy, all of which showed severe renal atrophy and loss of parenchyma. All specimens that included nonatrophic or partially atrophic renal tissue contained small medullary scars that involved only portions of the medullary pyramids. These sublobar medullary scars, which appeared linear and were typically discrete, extended from the inner medulla to the cortex. They obliterated collecting ducts, vasa recta and recurrent loops. The cortical portions of the scars contained remnants of nephrons and variable infiltrates of chronic inflammatory cells with lymphoid follicles. Seven of the specimens also contained acute disruptive ductal lesions with histopathological features characteristic of intrarenal reflux. We believe that the linear scars are the result of single duct medullary disruptions, mediated perhaps through obstruction of the several thousand nephrons subtended by each papillary duct and perhaps through localized disruption of the renal microvasculature. These sublobar scars accumulate as scarring progresses to end stage renal atrophy.