Mesoporous HAp aggregates were composed of needle-like crystals that were aligned to the c-axes direction perpendicular to the flat surface of plate-like aggregates. The pore size distributions of the HAp aggregates increased with increasing heat treatment temperature e.g. 3-20 and 26-52 nm, respectively, before and after heat-treated at 600 °C. The adsorption proteins on the mesoporous HAp aggregates were investigated by liquid chromatography using the HAp aggregates as an adsorbent. Elution molarity ratios of acidic proteins on the mesoporous HAp aggregates before and after heat-treatment at 600 °C increased with increasing molecular weight in the order of ferritin > fibrinogen > catalase > albumin, whereas the elution molarity ratios of basic proteins were considerably lower than those of acidic proteins. These results suggested that penetration of the large size acidic proteins into the pore of the as-prepared mesoporous HAp aggregate was slightly inhibited but were the proteins could easily penetrate into the pore of the heat-treated mesoporous HAp aggregates and then were selectively adsorbed on the mesoporous wall consisting of the a-surface of the HAp aggregate. Conversely, the basic proteins could be adsorbed on the wide outer surface of the plate-like HAp aggregates. Therefore, the elution molarity ratios of basic proteins decreased with decreasing the specific surface area by the heat treatment, independent of the mesoporous structure.