Fourier transform infrared spectroscopy (FT-IR) has gained popularity in the wine sector due to its simplicity and ability to provide a wine’s fingerprint. For this reason, it is often used for authentication and traceability purposes with more than satisfactory results. In this review, an outline of the reasons why authenticity and traceability are important to the wine sector is given, along with a brief overview of the analytical methods used for their attainment; statistical issues and compounds, on which authentication usually is based, are discussed. Moreover, insight on the mode of action of FT-IR is given, along with successful examples from its use in different areas of interest for classification. Finally, prospects and challenges for suggested future research are given. For more accurate and effective analyses, the construction of a large database consisting of wines from different regions, varieties and winemaking protocols is suggested.