Natural isothiocyanates, present in cruciferous vegetables and synthetic phenylhexyl isothiocyanate (PHI) are chemopreventive agents which act by blocking the initiation of carcinogen-induced tumors in rodents. We have demonstrated that isothiocyanates are also growth regulators, inhibiting cell cycle cdk activity and up-regulating inhibitor p21WAF1 (p21) in cancer cells. The up-stream mechanism to modulate cell cycle progression remained to be elucidated. Here, we have demonstrated that exposure of HL-60 leukemia cells to PHI induced G1 arrest and apoptosis. The hypothesis that PHI inhibits cell growth via chromatin remodeling was investigated. PHI mediates the complex cross talk between chromatin and DNA, and it was demonstrated for the first time as an inhibitor of histone deacetylases (HDAC). Thus, the HDAC activity in PHI-exposed HL-60 cells was reduced. Additionally, PHI reduced the expression of HDAC and increased the level of acetyl transferase p300, in favor of accumulation of acetylated histones. Within hours, global acetylation of histones was enhanced. PHI further mediated selective alterations of histone methylation, with a pattern consistent to the marks of transcription competent chromatins. The relationship between acetylated histones and p21 was examined by chromatin immunoprecipitation (ChIP) assay. Chromatins from cells exposed to PHI contained more p21 DNA in the precipitates of hyperacetylated histones, indicating more accessibility of transcription machinery to the p21 promoter after chromatin unfolding. The cell cycle inhibitors were activated as a result. In contrast to the PHI-induced apoptosis in HL-60 cells, which was mediated by caspase-9 up-regulation and bcl-2 reduction, PHI did not induce significant apoptosis in the mononuclear cells from normal peripheral blood and bone marrow. The results revealed a potential selective effect of isothiocyanates to inhibit the growth of malignant cells.