BACKGROUND Untreated obstructive uropathy produces irreversible renal damage and is an important cause of pediatric renal insufficiency. This study was designed to evaluate the effects of stem cell injection on morphological and pathological changes in the rat kidneys with partial unilateral upper ureteric obstruction (PUUUO). METHODS Wistar rats (n = 30) were operated upon to create a PUUUO by the psoas hitch method and were randomized into Group I (control, n = 15) and Group II (stem cell, n = 15); at day 5, 10 and 15, a subgroup of rats (n = 5) from each group was killed and the kidneys harvested. Pathological and morphological changes in the harvested kidneys were studied and compared between the two groups. RESULTS Morphologically, at day 15, Group II had significantly (p = 0.04) greater cortical thickness (0.48 ± 0.17 vs. 0.38 ± 0.09 mm). Histologically, at day 5, Group II had significantly (p = 0.032) lower peri-pelvic fibrosis. Group II group showed greater peri-pelvic inflammation as compared to Group I (p = 0.05). At day 10, lower grades of peri-pelvic fibrosis (p = 0.08), interstitial fibrosis (p = 0.037) and tubular atrophy (p = 0.05) were seen in the Group II. At day 15, Group II demonstrated significantly lower parenchymal loss (p = 0.037), glomerulosclerosis (p = 0.08), interstitial fibrosis (p = 0.08), tubular atrophy (p = 0.08) and peri-pelvic fibrosis (p = 0.08). CONCLUSIONS In a rat model of PUUUO, stem cell injection prevented detrimental changes in renal pathology and preserved renal parenchymal mass.