Radiotherapy is not commonly used for the treatment of human hepatocellular carcinoma, due to its poor response rate and poor tolerance of normal liver to ionizing radiation. Recently developed microarray technology makes it possible to verify genes responsive to anticancer therapy of human cancers by simultaneous analysis of gene expression profiles. In the present study, the expression profile of radiation-responsive genes in human hepatocellular carcinoma was evaluated through time-dependent cDNA microarray analysis of expressional variation, following exposure to ionizing radiation. Upon exposure to radiation, more than 13% of genes in both radiation-resistant and -sensitive cells responded to radiation. Time-dependent analysis of radiation-responsive genes revealed that, irrespective of radiation sensitivity, greatly different subsets of genes sequentially participated in cellular response to radiation at their specific activation or deactivation time points. The majority of radiation-responsive genes were differentially but not commonly expressed between radiation-resistant and -sensitive cells. When these differentially regulated genes were classified according to their physiological and functional characteristics and radiation sensitivity, it was prominently obvious that DNA repair-promoting genes were up-regulated in radio-resistant cells and down-regulated or unchanged in radiation-sensitive cells. The present findings indicate that different subsets of genes are sequentially working and DNA repair capacity may control the radiation sensitivity of human hepatocellular carcinoma cells more than any other physiological factor.