Lambrusco is a Protected Designation of Origin (PDO) red wine of Modena (Italy) produced according to the production regulation (Decreto Ministeriale (DM) July 27, 2009; GU no. 184-187-188, 13/08/2009). Here the use of (1)H NMR spectroscopy as molecular fingerprints of several PDO Lambrusco wines was proposed to serve as indicators of authenticity and quality control. Application of partial least squares discriminant analysis (PLS-DA) revealed a good varietal discrimination by analyzing the low-frequency spectral region. This model explains 68.8% of the variance for the Y vector (classification factor: varietal source). In particular, the signals of 2,3-butanediol, lactic, succinic and malic acids, and threonine were found to be the most statistically significant variables in the model. These findings seem to be very promising in the attempt to extend the study to geographical discrimination.