In recent years, due to the significant development of instrumental techniques, clinical research has acquired many interesting tools and analytical platforms that can support the development of advanced diagnostic methods. Nevertheless, along with these attractive instrument possibilities and the pressure to implement the complementary descriptions of biological systems, there is a need for rational research planning and the effective analysis of complex experimental data, which aims to assess research hypotheses, create logical rules and expert systems that support the diagnostic process, and respects the environment by developing greener analysis methods. These aspects are addressed when appropriate chemometric methods are applied in the research process. This article aims to show when and how this can be done.