Recently we reported the identification and characterization of a novel cross-link lesion formed between two adjacent cytosines in d(CpC), which is the major product formed upon 365 nm photoirradiation of d(CpC) in the presence of 2-methyl-1,4-naphthoquinone. In this study we discuss the isolation and structure characterization of another cross-link lesion formed under the same irradiation condition. Electrospray ionization mass spectroscopy, tandem mass spectrometry and two-dimensional nuclear Overhauser effect spectroscopy results demonstrate that the C6 carbon atom of the 5′ cytosine and the N3 nitrogen atom of the 3′ cytosine are covalently bonded. In addition, the 5′ cytosine moiety is deaminated and the C5 carbon atom in this cytosine is oxidized to a carbonyl group.