The underlying etiological cause of non-hereditary colorectal cancer has yet to be determined. The adenoma-carcinoma sequence is widely accepted, however, a sole trigger has not been specified. Therefore, we sought to further define genotypic and phenotypic parameters that could be involved in promoting a possible infection, inflammation and hyper-proliferation, followed by the adenoma-carcinoma sequence. Expression of phenotype-related parameters for MHC class I (HLA-A N-20 and β2 microglobulin) and class II (HLA-DRα and HLA-DR) as well as CD45 and carcinoembryonic antigen (CEA) were investigated immunohistochemically in a series of 93 colorectal cancers. Additionally, in 49 of the tumours the MHC class II genotype was analysed. MHC class II genotype analyses revealed a tendency towards DRB1*08 and DQB1*04. A significant association among the MHC class I markers or the MHC class II markers was found. No difference in marker expression could be detected between tumour and stromal tissue, however a significant inverse expression existed for markers of the functionally different class I or II systems. With the exception of CEA, there was no correlation between expression of any marker and tumour grade. Only 2% of tumours expressed no markers for MHC class I and II. Further studies on MHC class I and II genotype and phenotype relation in colorectal cancer may help to identify trigger mechanisms for tumourigenesis, involved markers and possible mechanisms of subsequent immune escape.