Under specific acidic conditions, both malondialdehyde (1, MDA) and 4-hydroxynonenal (2, 4-HNE) react with N-methyl-2-phenylindole (3) to give the same chromophoric cyanine 4 with maximal absorbance at 586 nm. Under such conditions, the reaction of 3 with 4-HNE (2) as well as with alkanals yields a second chromophoric cyanine 10 with maximal absorbance at 505 nm. The influence of different acids, iron(III), and oxygen on the reaction of 3 with such aldehydes was studied in detail. Under anaerobic conditions, the acid-induced reaction of 4-HNE with 3 afforded three rapidly interconverting intermediates, 5-7. Their subsequent fragmentation to 4 and hexanal in the presence of iron(III) and oxygen is consistent with the tandem beta-fragmentation of an indolyl radical cation. 1-Indolylalkenes were identified as essential intermediates in the acid-induced reaction of 3 with alkanals. A very mild iron(III)-catalyzed fragmentation of these intermediates afforded the corresponding 3-formylindole 11 as the direct precursor of the 505 nm chromophore 10. Such reactions were markedly influenced by the nature of the acid. Contrary to the rapid chromogenic reaction of 4-HNE which was observed in the presence of methanesulfonic acid, the HCl-induced reaction of 4-HNE with 3 did not afford the 586 nm chromophore. Furthermore, hexanal did not yield the 505 nm chromophore 10 upon reaction with 3 in the presence of HCl, again in contrast with the rapid chromogenic reaction which was observed in the presence of methanesulfonic acid. Comparison of the reaction mixtures under the two assay conditions confirmed that the same intermediates were formed. We conclude that the nature of the acid plays a crucial role in the oxidative fragmentation of intermediates into chromophores, allowing the selective assay of MDA in the presence of 4-HNE, using HCl acidic conditions.