Protein HC (human complex-forming glycoprotein, heterogeneous in charge) is a member of the lipocalin superfamily of hydrophobic ligand-binding proteins. The quantitatively dominating blood plasma form of protein HC is a protein HC-IgA complex (HC-IgA), which is the fourth most abundant immunoglobulin species in plasma. A photodiode array detection system on-line with a high performance liquid chromatograph has allowed the identification of low amounts of a heterogeneous fluorescent chromophore covalently bound to HC-IgA, and displaying significant absorption in the visible region in resemblance to the free protein HC chromophore. Several structurally related chromophore-containing linked peptides, carrying 80% of the light absorption at 330 nm of HC-IgA, were isolated from a pepsin-produced protein HC-alpha 1-nonapeptide. Sequence analysis of these linked peptides demonstrated that the bond between protein HC and IgA represents a novel type of reduction-resistant linkage between polypeptide chains and involves the cysteine residue 34 of protein HC and the penultimate cysteine residue of the carboxyl-terminal part of one of the IgA heavy chains, as well as the heterogeneous fluorescent chromophore. The light absorption and fluorescent spectra of the chromophore-linked peptides were similar to those of native free protein HC.