Introduction: Erythropoietin is a glycoprotein hormone that is responsible for regulating the synthesis of red blood cells. Unfortunately, the ability of recombinant human EPO (rhEPO) to enhance haematopoiesis which increases the tissue oxygenation has led to its abuse in sports. The identification of rhEPO is very challenging due to its high similarity with endogenous EPO. EPO and rhEPO have high diversity of glycoforms that have different but overlapped pI. Currently, the standard procedure to detect EPO abuse in urine and blood samples is still utilising gel-based tools which have consistency and sensitivity issues. Glycoproteomic mass spectrometry on the other hand is the new approach in the search for biomarkers to differentiate recombinant EPO from the endogenous one. However, there is still a big gap of knowledge on the glycosylations of EPO that requires extensive profiling. Objective: To perform glycoproteomic profiling of endogenous and recombinant EPO. Methods: NanoLC-Orbitrap-MS/MS was performed on endogenous (uEPO) and several rhEPO (BRP, Mircera, NESP, and Epoetin Delta). The liquid chromatogram was used to illustrate the variations between the molecules in their glycopeptides/peptide retention patterns. Mass spectral data was submitted to a bioinformatic platform for peptide and glycosylation de novo sequencing.MALDI-qTOF-MS/MS was also employed in parallel for glycosylation profiling. Results & Discussion: BRP showed a similar chromatographic pattern as uEPO except for a few distinct peaks. PEGlylated EPO Mircera showed two different regions of chromatographic peaks because the hydrophobic PEGylated peptides were retained longer than the non-PEGlyated peptides. Epoetin Delta and NESP showed even greater variation in the chromatographic pattern compared to uEPO believed to be due to differences in glycosylations and peptide sequence, respectively. Meanwhile, MALDI mass spectrum differential analysis enables the determination of sugar residues attachment to BRP. Conclusion: Glycoproteomic mass spectrometric profiling holds the key to better discrimination between endogenous and recombinant EPO for anti-doping purposes. © 2014 Asian Pacific Tropical Medicine Press.