Principal component analysis (PCA) was used to identify the main sources of variation in the Fourier transform infrared (FT-IR) spectra of 329 wines of various styles. The FT-IR spectra were gathered using a specialized WineScan instrument. The main sources of variation included the reducing sugar and alcohol content of the samples, as well as the stage of fermentation and the maturation period of the wines. The implications of the variation between the different wine styles for the design of calibration models with accurate predictive abilities were investigated using glycerol calibration in wine as a model system. PCA enabled the identification and interpretation of samples that were poorly predicted by the calibration models, as well as the detection of individual samples in the sample set that had atypical spectra (i.e., outlier samples). The Soft Independent Modeling of Class Analogy (SIMCA) approach was used to establish a model for the classification of the outlier samples. A glycerol calibration for wine was developed (reducing sugar content < 30 g/L, alcohol > 8% v/v) with satisfactory predictive ability (SEP = 0.40 g/L). The RPD value (ratio of the standard deviation of the data to the standard error of prediction) was 5.6, indicating that the calibration is suitable for quantification purposes. A calibration for glycerol in special late harvest and noble late harvest wines (RS 31-147 g/L, alcohol > 11.6% v/v) with a prediction error SECV = 0.65 g/L, was also established. This study yielded an analytical strategy that combined the careful design of calibration sets with measures that facilitated the early detection and interpretation of poorly predicted samples and outlier samples in a sample set. The strategy provided a powerful means of quality control, which is necessary for the generation of accurate prediction data and therefore for the successful implementation of FT-IR in the routine analytical laboratory.