We studied the processing of amyloid β-peptides (Aβs) including Aβ1-40, Aβ1-42 and pAβ3-42 by rat neutral cysteine protease bleomycin hydrolase (BH) according to the methods of SDS-PAGE, HPLC and matrix-assisted laser desorption/inonization time-of-flight mass spectrometry (MALDI-TOF MS). BH significantly processed them by novel features of its diverse activities. It initially cleaved at two sites, His14-Gln15 and Phe19-Phe20 bonds, in Aβ1-40 and Aβ1-42 by endopeptidase activity. The resultant peptides were degraded to short intermediates then to amino acids by aminopeptidase and/or carboxypeptidase activities. Also, full-length Aβs were clipped at the carboxyl(C)-terminal region. On the other hand, BH cleaved at only the His14-Gln15 bond in pβA3-42 within A short period of the reaction by endopeptidase activity, and processed the intermediates in order by carboxypeptidase activity. On processing by BH, it found that both fibrillar Aβ1-40 and Aβ1-42 were more resistant than non-fibrillar peptides. These results indicate that the processing specificity of BH depends upon the structure and sequence of Aβs.