Abstract: The spatial organization of biological structures profoundly influences their function, making histopathology a cornerstone in disease diagnosis. However, there exists a pressing need for advanced technologies surpassing current methods to identify specific biomarkers and inform clinical decisions. Recent advancements in genomics and microscopy have given rise to Spatial Transcriptomics (ST), a suite of techniques capable of profiling RNA molecules within intact tissue architectures. While each ST method offers varying resolution, throughput, sensitivity, and biological breadth, all possess the potential to illuminate the influence of spatial localization on cell phenotypes and disease heterogeneity and outcome, thereby revolutionizing biomedical research. Taking a comprehensive approach to ST data analysis, we employ pathology-guided and tailored methodologies to unravel the transcriptional orchestration of tissue, microenvironment, cellular and molecular functions in spatial context. This presentation offers insights into leveraging ST as powerful tools to decode tissue pathology. Through examination of healthy tissues and complex disease states, such as colorectal cancer, it provides a roadmap for the characterization of compositional and organizational heterogeneity of tissues, as well as the emergence and progression of disease.