A DNA-based method has been applied to the identification of several musts and wines using microsatellite markers. DNA was extracted from the solid phases of sixteen monovarietal and five multivarietal musts (mixtures of two musts down to a 4:1 proportion) and they were genotyped at seven microsatellites through a multiplex PCR reaction and automated fluorescent detection. PCR multiplexing was successful in monovarietal musts, but should be used with caution with at least some markers and in multivarietal musts. The same extraction and detection methods were unsuccessfully applied to the solid and liquid phases of five monovarietal commercial wines, even after using different concentration procedures. Nucleic acids presence was then studied in a recent must, during the fermentation process, and during the subsequent steps of winemaking. Genotyping was possible in the resulting experimental wine until decanting, when the particles in suspension were removed. These results suggest that wine authentication through DNA analysis is not possible in commercial wines, in the tested conditions.