Cytochrome c and myoglobin have been used as two representative proteins for assessing three parameters for protein encapsulation in mesoporous silica, specifically protein purity, protein secondary structure and morphology of the host structure. These aspects have been evaluated in order to determine the factors that control adsorption onto mesoporous silicas (MPS). Among the various MPS evaluated, those with rod like structures exhibited the highest loading amount ca. 408 mg g Γ1 and 177 mg g Γ1 for unpurified and ca. 241 mg g Γ1 and 106 mg g Γ1 for purified cytochrome c and myoglobin, respectively. These proteins were also found to be strongly adsorbed onto the silicas as indicated by low levels of leaching even after 10 h of extraction. The stability of proteins during the course of encapsulation experiments was confirmed by evaluating their secondary structure and moreover, the structural integrity of MPS before and after encapsulation was monitored by XRD. The results indicated at least a partial degradation of the mesoporous structure in case of protein bound MPS. In view of these observations, the accessibility of MPS channel structure is evaluated and their promise as hosts for biomolecule adsorption is assessed.