The present study aims to demonstrate the potential use of short-wave near infrared spectroscopy for the quality control of raw cow milk samples, collected from high mountain areas. The sampling plan comprised three farms, all located within the same Alpine region (South Tyrol, Italy), but located at different altitudes (1900 m, 1050 m and 950 m a.s.l). Each farm used a similar extensive grassland-based farming system. For comparison, raw milk samples were also collected from a farm located in the valley (Milan, Italy), at 200 m a.s.l. and subjected to an intensive farming system. From each location, the samples were collected 10 times within one month of production. All the milk samples were analysed by diffuse trans-reflectance in the wavelength range from 850 to 1350 nm. Principal component analysis of the spectra revealed that the short-wave near infrared bands, respectively, 847, 1084, and 1095 nm, were the most important to distinguish milk between farms. The signal intensities of these wavelengths were used to build a multivariate control chart based on the Hotelling T2 statistic. The results showed that short-wave near infrared spectroscopy can be successfully used to monitor milk products in a fast, simple and on-line way.