Aim of the study The task of long noncoding RNAs (lncRNAs) as a prospective goal for hepatocellular carcinoma (HCC) is a candidate for research. Several lncRNAs are involved in signal transduction, directing gene expression and epigenetic alteration in normal and cancer cells. Dysregulation of diverse lncRNAs has been involved in the pathogenesis and progression of different cancers including HCC. We aimed to investigate the differential expression of lncRNAs (aHIF, hPVT1, ANRIL) in HCC on top of chronic hepatitis C virus (HCV) and hepatitis B virus (HBV) infections. Material and methods 182 participants were included: 85 patients with HCC in addition to 50 patients with cirrhosis on top of chronic HCV or HBV, and 47 healthy subjects as controls. HCC was diagnosed by triphasic computed tomography (CT). Detection of α-fetoprotein (AFP) and serological markers of HCVAb and HBsAg by enzyme-linked fluorescent immunoassay (ELFA) and quantitation of lncRNAs by real time PCR were applied. Results Upregulation of ANRIL and hPVT1 and downregulation of aHIF were observed in patients with HCC on top of HCV and HBV vs. controls. Circulating aHIF could be of major diagnostic importance to discriminate HCC on top of HCV from cirrhotic patients with sensitivity 86.67% and specificity 91.89% whereas circulating hPVT1 had sensitivity 85.0% and specificity 84.62%; moreover ANRIL had AUC 0.902 and could discriminate HCC on top of HBV from cirrhotic patients. Conclusions The differential expression of lncRNAs (ANRIL, hPVT1 and aHIF) might be of major worth in predicting the occurrence of HCC in cirrhotic patients related to chronic viral hepatitis and could be beneficial in the early management.