Metabolic Syndrome (MetS) is a cluster of risk factors that increase the likelihood of heart disease and diabetes mellitus. It is crucial to get diagnosed with time to take preventive measures, especially for patients in locations without proper access to laboratories and medical consultations. This work presented a new methodology to diagnose diseases using data mining that documents all the phases thoroughly for further improvement of the resulting models. We used the methodology to create a new model to diagnose the syndrome without using biochemical variables. We compared similar classification models, using their reported variables and previously obtained data from a study in Colombia. We built a new model and compared it to previous models using the holdout, and random subsampling validation methods to get performance evaluation indicators between the models. Our resulting ANN model used three hidden layers and only Hip Circumference, dichotomous Waist Circumference, and dichotomous blood pressure variables. It gave an Area Under Curve (AUC) of 87.75% by the IDF and 85.12% by HMS MetS diagnosis criteria, higher than previous models. Thanks to our new methodology, diagnosis models can be thoroughly documented for appropriate future comparisons, thus benefiting the diagnosis of the studied diseases.