Several erythropoietin preparations (EPO) are used globally for anemia management. Repeated EPO use has been reportedly associated with thrombotic complications. Molecular profiles of these recombinant proteins vary widely, impacting their clinical profile. This may be due to cellular/receptor interactions and other modulatory properties. There are WHO and FDA regulatory guidelines regarding molecular profile; data on protein profiling is usually not provided by the manufacturers. Purpose of this investigation was to compare various clinically-used recombinant erythropoietin products Epogen (Amgen), Vintor (Emcure), Eprex (Janssen-CILAG) and Neo Recormon (Roche) utilizing protein chip array technology (Ciphergen, Fremont, CA). All products were analyzed using anionic SAX2 chips and molecular profile was obtained in the range of 0–150 KDa. Epogen and Vintor exhibited a main component at 32.4 KDa range with minor peaks at 13.5, 21.7 and 43.2 KDa. Intensity of the main component varied widely even within the 3 batches of Epogen. The Epogen preparations and Vintor brand contained albumin in different quantities. One batch of Epogen contained 4x higher amount of this material with a heterogeneous distribution. Epex and Neo Recormon did not have any albumin. One of the Epogen product also contained a component at 110.0 KDa. Glycosylation profiles of each of these preparations also differ. These data suggest that molecular heterogeneity exists within different recombinant erythropoietin preparations. Molecular heterogeneity among these preparations may be partly responsible for differential interactions within erythropoietin receptors on cells and anti-epo antibody generation. Protein chip array technology may be helpful in examining the protein components within different recombinant erythropoietins and may be helpful in establishing molecular profile guideline to minimize pharmacodynamic variance in erythropoietin preparations. Furthermore, molecular profiling of these recombinant proteins may be helpful in establishing the purity and homogeneity of these drugs.