Aplastic anemia (AA) is a potentially life threatening bone marrow disorder. The exact mechanisms responsible for AA pathogenesis are unclear and the disease is very difficult to study due to its rarity, heterogeneity in its pathology and limitations in number of cells available for examination. Our aim was to identify serum proteins differentially expressed in untreated AA patients compared to ATG treated patients and healthy controls that might be useful in understanding and monitoring AA. Serum was profiled on CM10 and Q10 ProteinChip arrays using SELDI-TOF/MS, detecting a number of differentially expressed protein peaks. A combined strategy of chromatographic fractionation, 1D gel electrophoresis, passive elution, trypsin digestion and LC-MS/MS analysis, formally identified two discriminatory peaks, further validated with immunodepletion, Western blot and ELISA. They include anti-inflammatory apolipoprotein A1 (APOA1), downregulated in AA compered to controls, and apolipoprotein C3 (APOC3), downregulated in AA compared to both control and ATG treated patients, and represent novel diseaseand therapy-associated AA biomarkers. Inflammatory biomarkers in AA serum support immune-mediated pathology of AA and suppressive action of ATG. Results presented here are the first to describe disease-and therapy-associated proteome changes in these patients. The two identified proteins are, to the best of our knowledge, the first reported serum biomarkers of AA. These biomarkers can potentially be used for disease detection, diagnosis and monitoring and can help in understanding the mechanism of AA. Further studies with additional samples are needed to confirm their importance in the pathogenesis of the disease and their clinical value.