To analyse the biological role of 5-methylation of cytosine residues in DNA requires precise and efficient methods for detecting individual 5-methylcytosines (5-MeCs) in genomic DNA. The methods developed over the past decade rely on either differential enzymatic or chemical cleavage of DNA, or more recently on differential sensitivity to chemical conversion of one base to another. The most commonly used methods for studying the methylation profile of DNA, including the bisulphite base-conversion method, are reviewed.