Imidazole dipeptides (IDPs) such as carnosine (CAR), anserine (ANS), and balenine (BAL) are widely distributed in the skeletal muscle of vertebrates. Recently, several studies have revealed that CAR plays an important role in the detoxification of cytotoxic aldehydes arising from the peroxide of unsaturated fatty acids and carbohydrate metabolite. Although intensive studies on the detoxification of aldehydes by CAR have been performed, few studies have focused on the effects of detoxification by ANS and BAL. To determine the potential of minor IDPs such as ANS and BAL to react with cytotoxic aldehydes, the present study was established to investigate the consumption of IDP after co-incubation with cytotoxic aldehydes using high-performance liquid chromatography (HPLC). In the case of unsaturated fatty acid-derived aldehydes such as 4-hydroxy-2-trans-nonenal (from n-6 fatty acid) and 4-hydroxy-2-trans-hexenal (from n-3 fatty acid), ANS and CAR decreased considerably after co-incubation, but BAL did not. In the case of 3-deoxyglucosone and methylglyoxal as carbohydrate metabolites, no IDPs decreased after co-incubation; however, the absorbance at 336 nm of the CAR and BAL mixtures increased dramatically in a time-dependent manner. In the case of glyceraldehyde, which is also a carbohydrate metabolite, all IDPs, especially BAL, decreased after co-incubation and a new peak, surmised to represent an IDP-glyceraldehyde adduct, appeared on the HPLC chromatogram. These results can help explain the unique function and behavior of ANS and BAL in specific species.