To investigate the association between viral infection pattern and hepatocellular carcinoma (HCC), 292 chronic hepatitis patients, including 108 with developed HCC were screened using serological and molecular genetics methods. Viral etiology was established in 267 (91.4%), anti-HCV detected in 198 (67.8%), and HBsAg in 124 (42.5%) including 93 (74.4%) cases with HDV co-infection. HCV mono-infection predominated in both, “non-HCC” and “HCC” groups (54% and 39%, respectively) with higher frequency in the first group (P = 0.011), whereas HBV in co-infection with HDV was more frequent in HCC group (14% vs 25%, P = 0.017). Patients with HCV mono-infection were older than those with co-infection (P<0.02), had higher frequency of HCV-viraemia (82% vs 7%, P < 0.0001), and yet had significantly lower prevalence of HCC (29.6% vs. 49.1%, P = 0.003). Alpha-fetoprotein (AFP) and protein induced by vitamin K antagonist-II (PIVKA-II) were specifically elevated in 71% of HCC patients. In conclusion, although HCV monoinfection pattern predominates in Mongolia, co-infection with HBV and HDV had stronger association with HCC development at younger age. Liver tumor markers; AFP and PIVKA-II are useful tools for complex HCC-screening and clinical follow-up for chronic hepatitis patients in Mongolia. J. Med. Virol. 78:1688–1695, 2006. © 2006 Wiley-Liss, Inc.