The last few years have seen a growing interest in the study of DNA methylation because of its now acknowledged implication in cancer. The use of bisulfite to convert unmethylated cytosine to uracil, even as methylated cytosine remains unchanged, constitutes the basis for differentiating between methylated and unmethylated specific CpG sites in CpG islands. This technique therefore is critical to the success of this approach. Different parameters have to be considered in order to achieve a total conversion of cytosines to uracils. Several bisulfite-based methods are available for analyzing DNA methylation status. Methylation-sensitive single-strand conformation analysis (MS-SSCA) yields specific and semiquantitative data. The method is based on bisulfite treatment of DNA followed by polymerase chain reaction using primers without a CpG site to avoid selective amplification of either methylated or unmethylated DNA, and finally by single-strand conformation analysis (SSCA). The method allows one to establish clonal variations in the DNA methylation status for clones representing as little as 5-10% of the total cell population. MS-SSCA has, furthermore, a broad application field since it is the appropriate method for the analysis of frozen, fixed, and even microdissected tissues