We evaluated the utility of SDS‐PAGE/Western blot and CE coupled with MS (CE‐MS) for detection of urinary polypeptide biomarkers of renal disease in patients with IgA‐associated glomerulonephritides. In a reference cohort of 402 patients with various renal disorders and 207 healthy controls, we defined CE‐MS patterns of renal damage and IgA nephropathy (IgAN). In a blinded analysis of a separate cohort of patients with IgAN (n = 10), Henoch‐Schoenlein purpura (HSP) with nephritis (n = 10), and IgA‐associated glomerulonephritis due to hepatitis C virus (HCV)‐induced cirrhosis (n = 9), and healthy controls (n = 12), we compared SDS‐PAGE/Western blot and CE‐MS against clinical urinalysis for detection of urinary proteins/polypeptides. Urinalysis indicated proteinuria for 50, 90, and 33% of patients, respectively, and for none of the healthy controls. SDS‐PAGE/Western blot showed urinary polypeptides abnormality for 90, 80, and 67% of patients, respectively, and for none of the healthy controls. CE‐MS indicated a Renal Damage Pattern in 80, 80, and 100 of patients, respectively, and in 17% of healthy controls, with the more specific IgAN Pattern in 90, 90, and 1%, respectively, and in none of the healthy controls. Based on differences in CE‐MS patterns, the disease mechanisms may differ among various IgA‐associated glomerulonephritides. These exploratory findings should be evaluated in a prospective study with contemporaneous renal biopsy and urinary testing. If validated, it may be feasible to adapt the CE‐MS methodology to develop novel tests to detect renal injury at earlier stages, assess clinical manifestations, and monitor responses to therapy in patients with IgA‐associated renal diseases.