Objective To review the relationship between histone modifications and gastrointestinal cancer. Methods Literatures on histone modifications and the relationship between histone modifications and gastrointestinal cancer were collected and reviewed. Results Histone modifications played an important role in the establishment of gene silencing during tumorgenesis. DNA methylation and histone modifications might interact with each other and form a complex network to establish and maintain gene silencing. Restoring gene function silenced by epigenetic changes in cancer had the potential of ‘normalizing’ cancer cells, which was named epigenetic therapy. Epigenetic therapy was very promising in prevention and treatment of gastrointestinal cancer, but many unsolved issues remain which need to be addressed in future studies. Conclusion Histone modifications are associated with the pathogenesis of gastrointestinal cancer. Restoring gene function silenced by epigenetic changes may have a great role in the prevention and treatment of gastrointestinal cancer.