Mucins are important in tumorigenesis and expressional alterations of mucins are common in human cancers. A membrane-bound mucin MUC15 and secreted mucins MUC4 and MUC7 are known to involve in tumorigenesis, but their mutation status in cancers remains unknown. Aim of this study was to explore whether MUC4, MUC7 and MUC15 genes are mutated and expressionally altered in gastric (GC) and colorectal cancers (CRC). In a public database, we found that MUC15 and MUC7 genes had mononucleotide repeats in the coding sequences that might be mutation targets in the cancers with microsatellite instability (MSI). We analyzed the mutations in 90 GC and 141 CRC (high MSI (MSI-H) or stable MSI/low MSI (MSS/MSI-L)) by single-strand conformation polymorphism analysis and DNA sequencing. In the present study, we found MUC15 frameshift mutations (14.7% of GC and 15.2% of CRC with MSI-H), MUC 7 frameshift mutations (2.9% of GC with MSI-H) and MUC4 frameshift mutations (8.8% of GC and 3.8% of CRC with MSI-H). These mutations were not found in in MSS/MSI-L (0/118). Additionally, we analyzed intratumoral heterogeneity (ITH) of MUC15 mutation in 16 CRC and found that seven CRC (43.8%) harbored regional ITH of MUC15. We also analyzed MUC15 expression in GC and CRC by immunohistochemistry. Negative MUC15 expression was identified in 15-41% of the GC and CRC irrespective of MSI status. Of note, the negative expression was more common in those with MUC15 mutations. We identified alterations of MUC genes at various levels (frameshift mutations, genetic ITH and expression loss), which together might play a role in tumorigenesis of GC and CRC with MSI-H. Our data suggest that mutation analysis in multiple regions is needed for a better evaluation of mutation status in CRC with MSI-H.