<i>Background:</i> In an immunofluorescence study using antibody to podocalyxin, we reported that urinary excretion of podocytes reflected podocyte injury in glomeruli. However, this method has some problems, since it is basically urine cytology. To overcome problems with this test, we measured whole podocalyxin content in urine sediment by enzyme-linked immunosorbent assay (ELISA). <i>Methods:</i> Urinary sediment podocalyxin (u-sed-PCX) content of the first morning urine was quantified by ELISA after solubilization by detergent. We measured urine samples from children with various glomerular diseases and from healthy volunteers as controls. The glomerular diseases were classified into two categories: group I (inflammatory glomerular, 5 diseases) and group II (non-inflammatory glomerular, 3 diseases). <i>Results:</i> (1) The level of u-sed-PCX was significantly higher in the urine from patients with glomerular diseases (groups I and II, median (interquartile range (IQR)): 2 (0.6–18.5), n = 111) compared with controls (0 (0–0.4), n = 135), and the level of u-sed-PCX in group I diseases (3.4 (0.6–27.2), n = 90) was significantly higher than those in group II diseases (0.9 (0.1–2.5), n = 21). (2) The presence of PCX in urine sediment was confirmed by Western blot analysis. (3) The degree of proteinuria was significantly correlated with the level of u-sed-PCX in group I (r_s = 0.539, p < 0.001), but not in group II. (4) In group I, the level of u-sed-PCX was significantly higher in the acute phase than in the chronic phase (p < 0.01). (5) Comparison of histological findings of renal biopsies with u-sed-PCX showed a significant correlation in acute extracapillary lesions (p < 0.05). (6) Persistent high level of u-sed-PCX paralleled good histological progression in renal biopsies. <i>Conclusion:</i> Quantification of urinary sediment podocalyxin by ELISA is a reliable and useful laboratory marker for the estimation of the severity of active glomerular injury and a urinary index of acute extracapillary changes.