Agricultural production seeks to obtain high quality, safe products for human consumption- a great concern for the dairy chain. The present investigation seeks to identify the correlation between the compositional and sanitary quality of raw milk (SCC/mL). The investigation was carried out in three districts of the Department of Nariño, Colombia. For this purpose, sampling and information collection was executed throughout the years 2016 and 2017. To determine the relationship between composition and sanitary quality, an analysis was made of the principal components of the milk, and a design of mixed models was creating using selected variables. The analysis showed that there is a relationship between the compositional variables, and the mixed model indicated that there is a significant relationship between the somatic cell count and the milk quality of the region. It was concluded that a somatic cell count above 500,000 CFU/mL has negative effects on protein, casein, and milk production.