The FTIR-ATR method coupled with the multivariate analysis of specific spectral areas of samples was developed to characterize two white grape varieties (Sauvignon Blanc and Hibernal) and two blue grape varieties (André and Cabernet Moravia) of wine planted and harvested in the Moravia region, Czech Republic. Principal component analysis and hierarchical cluster analysis were performed using fingerprint regions of FTIR spectra for all wines. The results obtained by principal component analysis in combination with linear discriminant analysis (PCA-LDA) scores yielded clear separation between the four classes of samples and showed very good discrimination between the wine samples, with a 91.7% overall classification rate for the samples. The conducted FTIR spectroscopy studies coupled with chemometrics allowed for the swift analysis of multiple wine components with minimal sample preparation. These methods can be used in research to improve specific properties of these wines, which will undoubtedly enhance the quality of the final wine samples obtained.