While typically found in cancers, frameshift mutations in microsatellites have also been detected in chronically inflamed tissues. Allogeneic hematopoietic cell transplantation (HCT) may potentially produce chronic tissue stress through graft-versus-host reactions. Therefore, we examined non-neoplastic epithelial tissues (colon, buccal) obtained 1 to 5061 days after human allogeneic HCT for the presence of genomic alterations at three tetranucleotide (SEE33, THO-1, D14S120) and three mononucleotide (ZP3, BAT26, SRY) microsatellite loci. All except two colon biopsies examined had histological signs of GvHD. No signs of mucositis or oral GvHD were present at the time of buccal sampling. Novel bands indicative of microsatellite instability (MSI) were detected in laser-capture microdissected (LCM) colonic crypts in 12 out of 16 patients (75%) and in buccal smears in 10 out of 24 (42%) allografted patients. In contrast to the allografted patients, no MSI was found in the LCM crypts obtained from 4 patients after intensive chemotherapy or from 7 control subjects with no history of either colon malignancy or chemotherapy, and in the buccal smears obtained from 8 patients after autologous HCT or from 9 healthy controls. MSI was found only at tetranucleotide markers but not at mononucleotides. There was no statistical correlation between the presence of MSI in colon and the underlying disease, the previous history of multiple (>=3) intensive chemotherapies before transplantation, the type of preparative regimen for HCT, the overall GVHD grade any time before sampling or the GvHD stage in colon at sampling. The MSI found in colon, which was often affected by graft-versus-host disease, was not due to loss of expression or nitrosylation of DNA repair proteins (MLH1, MSH2, MSH3, APE-1, XPA). There was no significant association between MSI in the buccal mucosa and patient age, gender, disease, type of conditioning, history of oral GvHD or overall GvHD occured at any point before buccal sampling. Interestingly, we found a significant association between the time of buccal sampling after transplantation and the presence of MSI (p=0.008). MSI was also found in three post-transplant squamous cell cancers examined. The frameshift alterations found in post-transplant tumors often differed from those in the associated non-malignant tissues. Our data show that genomic alterations in epithelium regularly occur after allogeneic HCT. This previously unacknowledged genomic instability after allogeneic HCT may be implicated in the evolution of post-transplant diseases, including secondary cancer.