The interaction of native bovine lactoperoxidase (nbLPO) with four substrates has been studied and compared with that of recombinant human myeloperoxidase (rhMPO). Kinetic, spectroscopic and binding parameters extrapolated for each enzyme-substrate adduct have been interpreted in the light of the structural data available for myeloperoxidase (X-ray structure) and lactoperoxidase (3D-model), respectively. The differences in the reactivity and affinity of nbLPO and rhMPO towards SCN(-), catechol, dopamine and 3,4-dihydroxyphenylpropionic acid are here discussed and related to a different structure of the organic substrate access channel as well as to a different accessibility of the heme pocket in the two enzymes.