Background: Familial adenomatous polyposis (FAP) and Gardner's syndrome (GS) are conditions, inherited in an autosomal dominant fashion, that predispose affected family members to the development of colorectal cancer. The gene(s) responsible for FAP/GS is on the chromosome 5q21-22. Several RFLP markers for the chromosome 5q21-22 region are now available and can be used clinically for premobid diagnosis in affected FAP/GS family members. Probe EF5.44 is an RFLP marker that is tightly linked (Lod Score>3.0) to the FAP/GS locus. Methods: In FAP family, 10 mL of peripheral blood was sampled from the index case, his parents, brother and sister, and his wife and children. In GS family, similiar amount of blood was sampled from the index case, his wife and children. DNA was purified and five micrograms of each DNA was digested with restriction enzyme Msp I, and Southern blotting and hybridization using the probe EF5.44 were performed. Results: Probe EF 5.44 yielded only one band of 2.0 Kb without RFLP in al1 FAP/GS family members of this studay. Conclusion: Probe EF5.44 was found to be uninformative in both FAP/GS family members of this study. These results reveal that linked DNA probe has several limitations due to it's inherent low heterozygosity and so new DNA markers, such as microsatellite VNTRs, are preferable for genetic linkage analysis.