We evaluated clinical significance of serum alpha-fetoprotein (AFP)-IgM immune complexes, in comparison with free AFP, on the diagnosis of primary hepatocellular carcinoma (HCC). Serum levels of AFP-IgM immune complexes and free AFP were determined by the ELISA method and electrochemiluminescence, respectively, in 103 healthy controls, 74 patients suffering from primary HCC, 27 patients suffering from liver cirrhosis, and 63 patients suffering from chronic hepatitis. The best cut-off value of AFP-IgM and free AFP for diagnosis of primary HCC were 300 AU/mL and 10 microg/L respectively, according to the area under the curve (AUC) in this study. The sensitivity of AFP-IgM and free AFP were 64.9 and 79.7%, and the specificity were 75.6 and 80.3%, respectively, when all cases of primary HCC were analyzed, and the AUC of free AFP was larger than that of AFP-IgM (0.85 vs. 0.72, Z=3.21). However, in case of primary HCC at early stages (stages I and II) were analyzed, the AUC of AFP-IgM was larger than that of free AFP (0.91 vs. 0.82, Z=1.73), which demonstrated that the sensitivity of AFP-IgM and free AFP were 94.4 and 72.2%, and the specificity were 81.9 and 79.9%, respectively. When both AFP-IgM and free AFP were positive, the specificity of diagnosis of primary HCC was 89.1%, and the efficacy was 79.0%. It is concluded that either sensitivity or specificity of serum level of AFP-IgM immune complexes was higher than that of free AFP in the diagnosis of primary HCC at early stages. As there was false positive AFP-IgM existed in the patients suffering from cirrhosis and chronic hepatitis, the combination of free AFP and AFP-IgM could significantly increase specificity and decrease false negative and/or false positive in the primary HCC at early stages.