Microsatellite instability (MSI) in colorectal tumours is demonstrated by PCR amplification of several different microsatellite loci. Minisatellites, which are repeats of longer sequences also found throughout the genome, may also be affected by tumorigenesis. Certain minisatellite alleles contain 2 types of similar repeat unit that are randomly interspersed. The interspersion pattern can be analysed by mapping variant repeat units along an amplified allele, minisatellite variant repeat unit mapping PCR (MVR-PCR). We have applied microsatellite analysis with 10 markers and MVR-PCR for locus D7S21 to 33 cases of colorectal neoplasia, 27 sporadic and 6 from patients suspected of having hereditary non-polyposis colorectal cancer (HNPCC). Of the 27 sporadic cases, 3 were MSI-high on microsatellite analysis and one MSI-low. Instability with MVR-PCR was observed, but only in the MSI-high cases. Four of the HNPCC patients had mismatch repair (MMR) gene mutations in either hMLH1 or hMSH2. All 4 had DNA instability by MVR-PCR, but only two of these had MSI (one high, one low). The other 2 of the 6 patients with suspected HNPCC were negative to mutation analysis. One had features strongly suggestive of HNPCC and was unstable by both microsatellite analysis (MSI-high) and by MVR-PCR. The other tumour, from an Amsterdam criteria positive kindred, did not demonstrate instability by any technique. Thus MVR-PCR detects DNA instability in MSI-high sporadic tumours and in those associated with HNPCC where MSI is observed. Further, in some MMR mutation positive cases MSI was not seen but instability was observed by MVR-PCR. MVR-PCR may be a valuable adjunct to the detection of MMR deficiency in colorectal tumours and it may allow new insights into the nature of DNA instability in this condition.