The effects of three common heat treatments (pasteurisation, boiling and autoclaving) on milk physicochemical properties and DNA quality were investigated. Milk composition, colour and pH value varied significantly during the heating process. The heat treatment also affected the DNA quality of the milk and, in particular, reduced the content of both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). These reached their lowest values when autoclaving was conducted, but the content of nDNA was never greater than that of mtDNA. The physicochemical and DNA quality changes in milk are crucial factors in any authentication process using polymerase chain reaction (PCR)‐based methods.