Alpha-fetoprotein (AFP) has been widely used as a diagnostic master for hepatocellular carcinoma (HCC), and the fucosylated fraction of AFP (AFP-L3) has been reported to be a specific marker for HCC. However, AFP-L3 has not always been reliable in cases with low serum AFP concentrations. Recently, a novel automated immunoassay for AFP-L3, the micro-total analysis system (mu-TAS), has been developed. The aim of this study is to evaluate the clinical usefulness of mu-TAS AFP-L3. Serum AFP-L3 was measured in 295 patients with HCC and in 350 with benign liver diseases. The diagnostic accuracy of mu-TAS AFP-L3 was compared with that of the conventional assay (liquid-phase binding assay; LiBASys). The relationship between mu-TAS AFP-L3 and clinical features was investigated. When the cutoff value was set at 7%, the sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of mu-TAS AFP-L3 were 60.0%, 90.3%, 76.4%, 83.9%, and 72.8%, respectively. Its sensitivity was particularly good (41.1%) in HCC subgroups with lower AFP concentrations (< 20 ng/ml). The positivity rates for mu-TAS AFP-L3 were higher at each tumor stage than those of LiBASys AFP-L3 (mu-TAS/LiBASys: stage I, 44.2%/16.3%; stage II, 52.9%/37.5%; stage III, 66.4%/44.5%; stage IV, 82.8%/65.5%). mu-TAS AFP-L3 is more sensitive for discriminating HCC than the conventional LiBASys AFP-L3, particularly in subgroups with lower AFP concentrations and early-stage HCC.