Abstract: The invention relates to a method for analyzing of determining the methylation pattern of a starting DNA and/or for distinguishing between methylated and non-methylated sites in the starting DNA, comprising at least (A) generating a first DNA fingerprint, containing bands corresponding to both the methylated and non-methylated sites of interest; and/or (B) generating a second DNA fingerprint, containing bands corresponding only to the methylated sites of interest; and optionally comprising (C) generating a third DNA fingerprint, containing bands corresponding only to the non-methylated sites of interest; and optionally further comprising (D) analysing the fingerprint(s) thus obtained. The fingerprints are preferably generated using AFLP, by means of a frequent cutter and a methylation sensitive rare cutter. The invention further relates to specific methods for generating the above first and second DNA fingerprint by means of AFLP, and kits for use with said methods.