The-Cancer-Genome-Atlas data on colorectal carcinoma have provided a comprehensive view of the tumor’s genomic alterations and their tumorigenic roles. Tumor morphology, however, has not been fully integrated into the analysis. The aim of this study was to explore relevant associations between tumor morphology and the newly characterized genomic alterations in colorectal carcinoma. Two-hundred-and-seven colorectal carcinomas that had undergone whole exome sequencing as part of The-Cancer-Genome-Atlas project and had adequate virtual images in the cBioPortal for Cancer Genomics http://www.cbioportal.org/ constituted our study population. Upon analysis, a tight association between “microsatellite instability-high histology” and microsatellite instability-high (p<.001) was readily detected and helped validate our image-based histology evaluation. Further, we showed: 1) among all histologies, the not-otherwise-specified type had the lowest overall mutation count (p<.001 for entire cohort, p<.03 for the microsatellite instable group), and among the microsatellite instable tumors, this type also correlated with fewer frameshift mutations in coding mononucleotide repeats of a defined set of relevant genes (p<.01); 2) cytosine-phosphate-guanine-island-methylator-phenotype-high colorectal cancers with or without microsatellite instability tended to have different histological patterns: the former more often mucinous and the latter more often not-otherwise-specified; 3) mucinous histology was associated with more frequent alterations in BRAF, PIK3CA, and the transforming-growth-factor-beta pathway when compared to non-mucinous histologies (p<.001, p=.01, and p<0.001, respectively); and 4) few colorectal cancers (<9%) exhibited upregulation of immune inhibitory genes including major immune checkpoints; these tumors were primarily microsatellite instable (up to 43%, versus <3% in microsatellite-stable group) and had distinctly non-mucinous histologies with a solid growth. These morphology-molecular associations are interesting and propose important clinical implications. The morphological patterns associated with alterations of immune checkpoint genes bear the potential to guide patient selection for clinical trials that target immune checkpoints in colorectal cancer, and provide directions for future studies.