Abstract Background. Hepatocellular carcinoma (HCC) had been recently classified as a complex disease with a wide range of risk factors. Analysis of AFP level as a tumor marker is applied in patients with a high risk of developing HCC. However, the lack of AFP sensitivity and specificity has elucidated the need for novel tumor markers. Therefore, the aim of the current study is to assess AFP, MAGE1 and MAGE 3, CK, and HCC cancer stem cell (CSC) markers (CD133, CD90, CD44) as potential biomarkers for HCC patients. Patients and Methods. This study was conducted on the peripheral blood lymphocytes (PBL) of one 130 participants involving 70 patients with HCC, thirteen patients with chronic hepatitis (CH) and 30 normal controls. For those patients, serum AFP was tested by ELISA. Telomerase, MAGE 1, and MAGE 3, CD90 and CD44 RNA expression was detected by qualitative reverse transcriptase-polymerase chain reaction (qPCR). CD133 and CK expression was measured by flowcytometry (FCM) and qPCR analysis in 10 ml of PBL of each patient. Results. All CH and HCC patients were positive for HCV antibodies. The number of cells expressing CD 133 in the patients PBL was significantly lower in HCC patients than other groups while that of CD90 and CD44 was significantly higher in HCC than in the other groups (p<0.01). Also, MAGE-1,MAGE-3, AFP, CD90 and CD44 expressions by qPCR were significantly higher (p<0.001) in HCC group than in chronic hepatitis and normal control groups. There was a highly significant difference (p<0.001) between groups for telomerase gene expression, which was detected in 10% and 42.3% of CHC and HCC patients respectively. The expression levels of AFP, CD44 and CD90 correlated significantly with HCC stage (r=.461, p=0.001), grade and multicentricity (r=.244, p=0.02) while CD133 showed a significant correlation with tumor size (r=.455, P=0.006) but not significantly correlated with multicentricity and HCC stage. Cellular expression of CK was significantly higher in HCC than in other groups, and showed a significant correlation with tumor size (r=.347, P=0.041) and multicentricity (r=0.513, P=0.02). Conclusion. 1) AFP, MAGE1, MAGE 3 and the number of cells expressing CK in the PBL of HCC could be used as markers for early detection of HCC. 2) The CSC markers (CD90, CD44) and AFP are highly expressed in HCC and contribute to aggressive phenotype thus they could be used as prognostic and predictive markers. Citation Format: Abdel-Rahman N. Zekri, Abeer Bahnassy. Evaluation of Alpha-fetoprotein (AFP), telomerase, melanoma associated antigen (MAGE1 and MAGE 3), cancer stem cell markers cytokeratin (CK) and (CD133,) as potential biomarkers for hepatocellular carcinoma (HCC). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3540. doi:10.1158/1538-7445.AM2013-3540