Calf thymus histones were found to be susceptible to a calcium-activated neutral protease [CANP: EC 3.4.22.17] which required a high concentration of calcium ions for its activity (mCANP). The susceptibilities of histones were in the order of relative degradation rate: H2B, H2A, and H3. The major peptide fragments released by CANP from H2A, H2B, and H3 were isolated and the cleavage sites were determined. Examination of amino acid sequences and environmental features around the cleavage site as well as kinetic analysis of the degradation process led us to the following conclusions about the mode of substrate recognition of mCANP: 1) The cleavage sites in histones could not be interpreted in terms of the primary structure around them. Thus, it seems unlikely that the specificity of CANP solely depends on its recognition of any specific amino acid residues or sequences. 2) The susceptible bonds were never located in the midst of either a hydrophobic or hydrophilic alignment of amino acid residues but in the vicinity of the boundary between hydrophilic and hydrophobic clusters. 3) Once a peptide fragment was generated by the proteolytic degradation, no further cleavage occurred even if the peptide still contained a bond corresponding to what was susceptible to CANP in an intact histone. This observation was interpreted to mean that CANP may recognize a certain higher order structure of its substrates.