We analyzed 29 Sialolith samples, employing classical Population Genetic principles (Hartl and Clark 1980 (1), Hahn 2018 (2)) and Systems Biology analysis (ed: by Rigoustsos and Stephanopoulos 2006 (3)) approaches to create specific algorithms designed for our research objectives. Using these methodologies, specific unknowns such as the intrinsic variability of salivary stones, the role that protein matrix plays in the structure and evolution of the stones, and the nature of their interaction with the inorganic phase were addressed. In addition, the genetic and bio-functional aspects as classifying parameters were included and established an experimental frame of comparisons.