Nonlinear optical microscopy techniques have emerged as a set of successful tools within the biomedical research field. These techniques have been successfully used to study autofluorescence signals in living tissues, structural protein arrays, and to reveal the presence of lipid bodies inside the tissular volume. In the first section, the nonlinear contrast technique foundations is described, and also, a practical approach about how to build and combine this setup on a single confocal system platform shall be provided. In the next section, examples of the usefulness of these approaches to detect early changes associated with the progression of different epithelial and connective tissular diseases are presented. Finally, in the last section, we attempt to review the present-day most relevant analysis methods used to improve the accuracy of multimodal nonlinear images in the detection of epithelial cancer and the supporting stroma. These methods are presented as a set of potential valuable diagnostic tools for early cancer detection and to differentiate clinical subtypes of osteogenesis imperfecta disorders, being highly advantageous over present classical clinical diagnostic procedures. In this chapter, it is proposed that the combination of nonlinear optical microscopy and informatics-based image analysis approaches may represent a powerful tool to investigate collagen organization in skin diseases and tumor cell morphology.