The aim of this study was to compare the nutritional composition of a genetically modified (GM) CMV-resistant red pepper strain with its parental line. Specifically, the nutrient content (moisture, protein, lipid, ash, carbohydrate, and energy), minerals, fatty acid composition, capsaicinoids (capsaicin and dihydrocapsaicin), free sugars (glucose, sucrose, and fructose), vitamin E isomers (${alpha}$-, ${eta}$-, ${gamma}$-, and ${delta}$-tocopherols), vitamin C, phytosterols (campesterol, stigmasterol, and ${eta}$-sitosterol), squalene contents, and ASTA values were analyzed and compared. Most of the analyzed compounds showed no significant differences between the GM red peppers and the parental line. The only significant difference was observed in stigmasterol content, but the difference was below the 15% natural-fluctuation threshold. These results suggest that the CMV-GM pepper is equivalent to its parental line in terms of nutritional and phytochemical composition.