To investigate a molecular basis for iron depletion in human hepatocellular carcinoma (HCC), 19 cases of HCC were analyzed by two-dimensional electrophoresis (2DE) and matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Results were compared with those of paired adjacent nontumorous liver tissues. Comparative analysis of the respective spot patterns in 2DE showed that tissue ferritin light chain (T-FLC), an iron-storage protein, was either severely suppressed or reduced to undetectable levels in HCC, which was further supported by Western blot and immunohistochemical analysis. In contrast, transferrin receptor (TfR) was shown to be overexpressed in the same HCC samples. Interestingly, the relative levels of messenger RNA (mRNA) expression of T-FLC in HCC, which were measured by a real-time quantitative reverse-transcription polymerase chain reaction (PCR), exhibited almost the same levels as those in normal tissues, suggesting that the translational or posttranslational modification of T-FLC may be the cause of T-FLC suppression in HCC. Furthermore, with PCR-based loss of heterozygosity analysis, only 1 of 19 HCCs showed chromosomal deletions at 19q13.3-q13.4 where T-FLC is located, indicating that the suppression of T-FLC is unlikely due to structural genomic changes with HCC. In conclusion, both proteomic and genomic evidence support not only a basis for the suppression of T-FLC in HCC but also provide a new clue to the unresolved question of iron depletion during hepatocarcinogenesis.