Purpose Clarify the differences between Familial Adenomatous Polyposis (FAP)-associated Congenital Hypertrophy of the Retinal Epithelium (CHRPE) and benign variants with regards to lesion characteristics and associated risk. Observations An eighteen-year-old man with no past medical history was found to have multiple lesions in both eyes that were consistent with FAP-associated CHRPE. Although family history was negative for colon cancer, a colonoscopy was performed, and hundreds of polyps were found extending from the rectum to the distal colon with pathological findings of tubular adenoma. Genetic testing was consistent with a possible de novo Adenomatous Polyposis Coli (APC) mutation. Conclusions FAP is an autosomal dominant syndrome that causes colorectal cancer by age thirty-five in ninety-five percent of cases. There has been no established relationship between the benign variants of CHRPE and FAP, and patients with benign variants have no increased risk of colon cancer. While the lack of distinction in nomenclature and similar lesion appearance often leads to misdiagnosis and overtreatment, there are distinct ocular exam features that can provide the correct diagnosis. The exam findings that distinguish FAP-associated CHRPE lesions are (1) bilateralism, (2) occurrence in multiple quadrants, (3) pisiform shape, and (4) irregular borders. Knowing these features can be of great aid, especially in the setting of suspected de novo Familial Adenomatous Polyposis.