Plant genetic engineering research has been used to confer metabolic pathways to fortify nutritional traits of crops. In these metabolically engineered crops, endogenous metabolic status should be inevitably influenced by the newly designed and introduced enzymatic steps with the aid of metabolic genes from other organisms. Here, we report metabolomic and proteomic comparisons between genetically modified (GM) high astaxanthin-producing lettuce (Lactuca sativa L.) that was generated with chloroplast transformation and its parental cultivar, together with commercial lettuce varieties as controls. It was demonstrated that the higher adenine levels in the GM lettuce samples were the only difference consistently observed between the GM and control lettuce samples. In addition, no significant differences were observed in the levels of nitrate-nitrogen and the allergenic protein Lac s 1. These results indicate that the endogenous metabolic status of lettuce is not noticeably modified by genetic engineering of the high astaxanthin-producing trait.