OBJECTIVE To assess recovery of renal parenchymal thickness and urinary protein levels in patients with severely hydronephrotic kidneys after nephrostomy placement. METHODS Fourteen patients (median age 1 year, range 6 months-7 years) who underwent nephrostomy placement for unilateral ureteropelvic junction obstruction at our hospital between May 2007 and January 2009 were included in a retrospective analysis. All patients had severe hydronephrosis, with a median parenchymal thickness of 1.8 mm (range 1-2.5 mm). Kidney morphology was examined by ultrasound before the procedure and 1, 2, 3, 4, 6 and 8 weeks after. Urinary proteins (including albumin, immunoglobulin [IgG], alpha2-macroglobulin, alpha1-microglobulin, beta2-microglobulin [beta2-MG] and kappa chain) and creatinine levels were also tested during these follow-up visits. Fifteen healthy children were assessed for urinary protein levels as well and made up the control group. RESULTS Parenchymal thickness increased within 4 weeks of nephrostomy placement. Kidney volumes were significantly decreased within 2 weeks. No further changes in morphology were detected after 4 weeks. Urinary alpha1-microglobulin and beta2-MG levels decreased to baseline within 1 and 4 weeks, respectively. Urinary albumin, IgG, alpha2-macroglobulin and kappa chain levels decreased gradually after nephrostomy, but did not return to baseline within 8 weeks. CONCLUSIONS After nephrostomy placement, parenchymal thickness increases within 4 weeks, tubular function returns to normal earlier than glomerular function and glomerular membrane repair is inversely correlated with the severity of damage.