Abstract: The invention provides a new method of determining the presence of one or more polymorphic sites in a target nucleic acid sequence. The method comprises determining changes in the melting profile of an amplified product where the amplified product was amplified with a primer pair where one of the primers is labeled, e.g., with a fluorescent label. The method employs a probe that is labeled with a label that interacts with the label on the primer, e.g., a quencher that quenches the fluorescent label on the primer, such that the signal is quenched when the probe and primer are in close proximity. A change in the melting profile of an amplified product in comparison to a control reflects the presence of the polymorphic site.