Background: Podocyte depletion causes glomerulosclerosis, and persistent podocyte loss drives progression to end-stage kidney disease. Urinary sediment podocyte (u-sed Pod) mRNA excretion and urinary supernatant podocyte (u-sup PCX) protein have been used to monitor disease activity in glomerular diseases. However, the differences in these markers among pathologies have not been investigated. We examined the roles of these markers in kidney diseases. Methods: From January 2013 to March 2016, early morning urine samples were collected from 12 healthy controls and 172 patients with kidney disease (minor glomerular abnormality with mild proteinuria and/or microscopic hematuria, n = 15; minimal change nephrotic syndrome [MCNS], n = 15; membranous nephropathy [MN], n = 15; IgA nephropathy [IgAN], n = 60; crescentic glomerulonephritis [Cres GN], n = 19; lupus nephritis [LN], n = 10; others, n = 38). We examined u-sed Pod mRNA excretion, u-sup PCX protein and the urinary protein:creatinine ratio (u-PCR). Results: U-sed Pod mRNA excretion was significantly correlated with u-sup PCX protein (r = 0.37, p < 0.001). Both u-sed Pod mRNA excretion and u-sup PCX protein were significantly correlated with u-PCR (r = 0.53, p < 0.001 and r = 0.35, p < 0.001, respectively). Interestingly, u-sed Pod mRNA excretion was significantly increased in proliferative-type glomerulonephritis-including IgAN with extracapillary proliferative lesions, Cres GN and LN class IV-and significantly correlated with the rate of crescent formation, whereas u-sup PCX protein was significantly increased only in MN and subepithelial dense deposit-type LN compared with controls. Conclusions: Higher u-sed Pod mRNA excretion and u-sup PCX protein were associated with proliferative-type glomerulonephritis indicating podocyte detachment and subepithelial dense deposit-type glomerulonephritis, respectively. The results suggest that u-sed Pod mRNA excretion and u-sup PCX protein have usefulness for the diagnosis and measurement of disease activity with regard to glomerular diseases.