Abstract Background: HCC is the most common primary liver malignancy. Understanding the crosstalk of Mitophagy-related genes and apoptosis in the development of cancer can lead to finding out new biomarkers which will help in early detection of HCC. Aim of Study: This study aimed to retrieve novel RNA based network related to mitophagy and apoptosis characteristic for HCC development from public microarray databases. Material and Methods: Quantitative assessment of serum NFYA and TOMM40 gene expression was performed by qRT-PCR. Fifty-six patients diagnosed HCC, nineteen chronic hepatitis C cases and seventeen healthy volunteers. Results: ROC curve analysis was performed to evaluate the diagnostic value for NFYA with AUCs=0.97, cutoff point of >!1.3, sensitivity 96.5 %, specificity 94.4%, PPV 93.3%, NPV 97.1% and accuracy 95.7%. TOMM40 had AUC=0.83 and a cutoff point of !90.82, sensitivity 82.7%, specificity 77.7%, PPV 75%, NPV 84.8% and accuracy 80.2%. NFYA expression were significantly higher in HCC patients compared to CHC group and control group with p-value <0.001*. Also, TOMM40 level showed highly significant difference between HCC group and CHC group (p<0.01) and there was also a significant difference between CHC group and control group as regards fold change of serum TOMM40 (p<0.05). Conclusion: Our data suggest that NFYA and TOMM40 expression levels could be highly accurate, early and non-invasive biomarkers in HCC diagnosis. It is promising as a general strategy for future panel biomarker development in the serum of HCC patients and CHC patients.This can over-come the lower reliability of single-gene biomarker experi-ments while maintaining high accuracy by combining signals from multiple genetic levels.