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Food adulteration is an issue of major concern, as numerous foodstuffs and beverages do not follow their labeling. Our research interest is in the field of authenticity of dairy products and particularly cheese. Adulteration of dairy products is a well-known phenomenon, and there are numerous published studies specifically on the authenticity of cheese. In fact, substitution of a portion of fat and/or proteins, adulteration with milk of other species' origin, and mislabeling of ingredients are some of the main issues that the science of dairy products' authenticity is regularly facing. Discrimination of dairy products can be determined through several chemical or microbiological methods as presented in the literature. In addition, chemometric analysis is an important tool for interpretation of a huge load of measurements. The aim of this study is to discriminate between various milk samples, which is the primary ingredient of dairy products. Milk samples with different trademarks were analyzed. That data was combined with Halloumi cheese samples for chemometric discrimination of species' origin. The innovative point of this study is the fact that it is the first time that a research study related to dairy products includes Halloumi cheese which is a traditional Cypriot cheese, not well-studied until now. The first step of the methodology was the freeze-drying via lyophilization of the samples. Fourier transformed infrared spectroscopy (FTIR) was chosen for their chemical characterization. Moreover, interpretation of the measurements was carried out by chemometric analysis using SIMCA software. For this study, FTIR data combined with chemometrics have given a very good discrimination of the samples according to their species' origin. Chemometric methods such as PCA and OPLS-DA have been used with great success. In the future, this model will be studied regarding geographical origin of the samples., (© 2020 The Authors. Food Science & Nutrition published by Wiley Periodicals LLC.)