Patients between 18 and 80 years of age who have received a HSCT and developed oral cGVHD-related stomatitis as confirmed by surgical biopsy may be eligible for this study. The only eligible female participants for the pilot study will be women who are unable to have children. In the pilot study, participants will be randomly assigned to receive thalidomide gel 20mg or placebo (a gel with no thalidomide) to use four times a day for 4 weeks. In the mouthwash study, participants will be randomly assigned to receive 0.1% 20mg thalidomide mouthwash or placebo (a mouth rinse with no thalidomide) to use four times a day for 4 weeks.