Abstract: Provided herein are methods for the analysis of methylation in nucleic acid molecules, comprising bisulfite conversion and subsequent copying or amplification in the presence of a ligand-labelled dCTP or a ligand-labelled dGTP incorporated at the site of a cytosine or complementary guanine, respectively, at positions corresponding to methylated cytosines in the bisulfite-treated nucleic acid or after the copying or amplification, subjecting the resulting nucleic acid molecules to restriction endonuclease digestion with an enzyme which comprises a cytosine nucleotide in its target recognition sequence to generate nucleic acid fragments with termini proximal or adjacent to one or more cytosines and attaching a ligand or oligonucleotide adaptor and subsequently amplifying the nucleic acid molecules.