A method and apparatus for the detection of polymorphisms in a nucleic acid sample (e.g. blood, sperm, saliva, cells, . . . ). To enhance the efficiency and the reliability of the known methods (e.g. DGGE, SSCP and TGGE) the amplification process (e.g. PCR) preceding the actual detection step is performed in or on the polyacrylamide gel. Multiple gradients (of chemical denaturants, thermal denaturants and of porosity of the gel matrix) are used for the separation of DNA fragments, by zone electrophoresis on gel slabs or by capillary electrophoresis.