Background: The hepatokine fetuin-A, released by the human liver, promotes pro-inflammatory effects of perivascular fat. The involvement of inflammation in type 2 diabetes mellitus (T2DM) can affect the kidney and contribute to the development of diabetic kidney disease. Therefore we examined the association of urinary fetuin-A protein fragments with renal damage in T2DM patients. Methods: Urinary peptides of 1491 individuals using proteome data available from the human urine proteome database were analysed. Prediction of proteases involved in urinary peptide generation was performed using the Proteasix tool. Results: We identified 14 different urinary protein fragments that belong to the region of the connecting peptide (amino acid 301-339) of the total fetuin-A protein. Calpains (CAPN1 and CAPN2), matrix metalloproteinase and pepsin A-3 were identified as potential proteases that were partially confirmed by previous in vitro studies. Combined fetuin-A peptides (mean of amplitudes) were significantly increased in T2DM patients with kidney disease and to a lesser extent with cardiovascular risk. Furthermore, fetuin-A peptide levels displayed a significant negative correlation with baseline estimated glomerular filtration rate (eGFR) values (r = -0.316, P < 0.0001) and with the slope (%) of eGFR per year (r = -0.096, P = 0.023). A multiple regression model including fetuin-A peptide and albuminuria resulted in a significantly improved correlation with eGFR (r = -0.354, P < 0.0001) compared with albuminuria, indicating an added value of this novel biomarker. Conclusions: The urinary proteome analysis demonstrated the association of fetuin-A peptides with impaired kidney function in T2DM patients. Furthermore, fetuin-A peptides displayed early signs of kidney damage before albuminuria appeared and therefore can be used as markers for kidney disease detection.