Production processes influence both the composition and microstructure of cheese. Frequently the relationship between property, processing and structure has been studied empirically and the complex interactions between all parameters have not been quantified. This is often due to the limited number of production processes used to produce samples which may potentially produce biased correlations. In this study mozzarella cheeses were manufactured with a range of compositions and production processes to give three groups of cheeses with different fat contents, draining pH or calcium contents, and stretching conditions, i.e. stretching temperature and speed. Principal Component Analysis was applied to the analysis of correlations within each group of cheese samples. In this study, we found that a positive correlation exists between the diameter of fat globules and meltability, as well as free oil. In addition, we also found a positive correlation between the protein content and stretching parameters.