Microsatellite-stable, near-diploid (MSIÀCINÀ) colorectal carcinomas have been reported, but it is not clear as to whether these tumours form a discrete group or represent one end of the distribution of MSIÀCIN þ cancers. In order to address this question, we screened 23 MSIÀCINÀ colorectal cancers for gains and losses using array-based comparative genomic hybridization (aCGH) based on large-insert clones at about 1 Mb density. We compared our findings with those from a small set of MSI þ CIN þ cancers, and with our reported data from MSIÀCIN þ and MSI þ CINÀ cancers. We found no evidence of any form of genomic instability in MSIÀCINÀ cancers. At the level of the chromosome arm, the MSIÀCINÀ cancers had significantly fewer gains and losses than MSIÀCIN þ tumours, but more than the MSI þ CINÀ and MSI þ CIN þ lesions. The chromosomal-scale changes found in MSIÀCINÀ cancers generally involved the same sites as those in MSIÀCIN þ tumours, and in both cancer groups, the best predictor of a specific change was the total number of such changes in that tumour. A few chromosomal-scale changes did, however, differ between the MSIÀCINÀ and MSIÀCIN þ pathways. MSIÀCINÀ cancers showed: low frequencies of gain of 9p and 19p; infrequent loss of 5q and a high frequency of 20p gain. Overall, our data suggested that the MSIÀCINÀ group is heterogeneous, one type of MSIÀCINÀ cancer having few (p6) chromosomal-scale changes and the other with more (X10) changes resembling MSIÀCIN þ cancers. At the level of individual clones, frequent and/or discrete gains or losses were generally located within regions of chromosomal-scale changes in both MSIÀCINÀ and MSIÀCIN þ cancers, and fewer losses and gains were present in MSIÀCINÀ than MSIÀCIN þ tumours. No changes by clone, which were specific to the MSIÀCINÀ cancers, were found. In addition to indicating differences among the cancer groups, our results also detected over 50 sites (amplifications, potential homozygous deletion and gains or losses which extended over only a few megabases) which might harbour uncharacterized oncogenes or tumour suppressor loci. In conclusion, our data support the suggestion that some MSIÀCINÀ carcinomas form a qualitatively different group from the other cancer types, and also suggest that the MSIÀCINÀ group is itself heterogeneous.