Aim: The study assessed mRNA expression of podocyte-associated molecules in urinary sediments of patients with type 2 diabetes mellitus (DM) in relation to urinary podocytes, biomarkers of podocyte injury and of proximal tubule (PT) dysfunction. Methods: A total of 76 patients with type 2 DM and 20 healthy subjects were enrolled in a cross-sectional study, and assessed concerning urinary podocytes, urinary mRNA of podocyte-associated genes, urinary biomarkers of podocyte damage and of PT dysfunction. Results: We found significant differences between urinary mRNA of podocyte-associated molecules in relation with albuminuria stage. In multivariable regression analysis, urinary mRNA of nephrin, podocin, alpha-actinin-4, CD2-associated protein, glomerular epithelial protein 1 (GLEPP1), ADAM 10, and NF kappa B correlated directly with urinary podocytes, albuminuria, urinary -alpha1-microglobulin, urinary kidney-injury molecule-1, nephrinuria, urinary vascular endothelial growth factor, urinary advanced glycation end-products (AGE), and indirectly with eGFR (p < 0.0001, R-2 = 0.808; p < 0.0001, R-2 = 0.825; p < 0.0001, R-2 = 0.805; p < 0.0001, R-2 = 0.663; p < 0.0001, R-2 = 0.726; p < 0.0001, R-2 = 0.720; p < 0.0001, R-2 = 0.724). Conclusions: In patients with type 2 DM there is an association between urinary mRNA of podocyte-associated molecules, biomarkers of podocyte damage, and of PT dysfunction. GLEPP1, ADAM10, and NF kappa B may be considered additional candidate molecules indicative of early diabetic nephropathy. AGE could be involved in this association.