Barley is the cereal par excellence in the production of malt for beer and other alcoholic beverages. Inthis work, biochemical (hordein A-PAGE) and molecular (RAPDs, AFLPs) markers have beencompared for their efficiency in malt fingerprinting. To overcome the difficulties related to the qualityof the DNA extracted from grain malt, malted coleoptiles are proposed as useful tissue for theextraction. On the basis of our data, we exclude a fingerprinting system based on A-PAGE hordeinanalysis because of the degradation of these proteins during the malting process. Comparing molecularmarkers for their efficiency and repeatability, we indicate AFLP analysis based on template DNAextracted from the tissue of grain malt coleoptile as an excellent tool for malt fingerprinting.