In families at risk for hereditary non-polyposis colorectal cancer (HNPCC) that do not fulfill all clinical criteria for HNPCC, additional evidence is sought by testing cancer specimens for microsatellite instability (MSI). We investigated whether the location of a colorectal cancer (CRC) predicts the result of MSI-testing in these families. One hundred and seven patients suspected for HNPCC were offered MSI-testing. MSI-testing was positive in 6/7 patients with endometrial carcinoma and in 22/100 patients with CRC. Only one out of 22 (4%) rectal cancers was MSI-positive, and in this patient no mismatch repair (MMR) gene mutation was found. Right-sided colon carcinomas were more likely to be MSI-positive (14/37 or 38%), followed by left-sided colon carcinomas (7/4 or 17%) (p < 0.05), with 6/14 and 4/7 MMR gene mutations, respectively. The likelihood that a tumor would be MSI-positive was 3.3 times greater for right-sided than for left-sided colon cancer (OR 3.3, p < 0.05). Microsatellite instability was 8.1 times more frequent in colon cancers than in rectal cancers (p < 0.05). The presence of MSI was independently related to fulfillment of the Bethesda criteria (OR 7.0, p = 0.01). In families with multiple cases of colorectal cancer, the rectal cancers are only rarely MSI-positive. This indicates that even in families with multiple colorectal cancers, rectal cancers are most commonly of sporadic origin.