Characterization of wine vinegars qualified with a Protected Designation of Origin (PDO) is crucial to certify their quality and authenticity. Spectroscopic techniques as Fourier transform mid infrared spectroscopy (FTIR) with Attenuated Total Reflectance (ATR) has been applied to investigate its potential as a rapid, cost-effective and non-destructive tool for characterizing different categories of high-quality vinegars. Spectra from 67 wine vinegars belonging to the PDOs “Vinagre de Jerez” and “Vinagre Condado de Huelva”, including their different established categories, were analyzed in the 4000–600 cm−1 infrared region. Changes associated to categories were observed in the region 1800–900 cm−1. These changes were assigned to certain compounds that increase during aging (e.g. acetic acids, alcohols, esters) or are characteristic of Pedro Ximenez category (e.g. sugars, furfural). Principal component analysis carried out on the most relevant spectral features, revealed that aging of vinegars clearly affect the ATR-FTIR spectra obtained in each PDO