A rapid procedure for isolating genomic DNA from milk samples has been devised, based on the use of Chelex resin. By using this protocol, genomic DNA was extracted from milk samples from 15 cows and 15 goats. The suitability of these DNA preparations as a template for performing the polymerase chain reaction (PCR) was tested by amplifying three different loci of the bovine genome: exon 4 of the κ-casein gene and the INRA5 and INRA23 microsatellites, together with two others: exon 19 of the αs1-casein gene and exon 2 and part of intron 2 of the DRB gene of the caprine genome. No amplification products could be obtained from any samples at 30 cycles. In contrast, at 45 cycles the number of amplified samples ranged from 86 to 100% and at 65 cycles all the DNA targets were amplified, indicating that the number of cycles was a critical factor to be optimized for obtaining the desired PCR target. These results suggest that this method may be a useful tool for analysing genetic polymorphism at the DNA level by PCR and relating it to milk composition and other traits of economic interest.