Utilizing polypeptide secondary structure as a means for controlling oxide pore architectures is explored. Poly-L-lysine is used as a model polypeptide as its folding behavior is well understood and compatible with the sol-gel chemistry of silica. Here, we show that silicas synthesized with poly-L-lysine in a alpha-helix conformation possess cylindrical pores that are approximately 1.5 nm in size, whereas silicas synthesized with poly-L-lysine in a beta-sheet conformation possess larger pores, the size of which are a function of the poly-L-lysine concentration, or in other words the size of the aggregate. In both cases, highly porous materials are obtained. In-situ circular dichroism measurements of the synthesis mixtures show that the poly-L-lysine secondary structure is not perturbed during synthesis. Infrared spectroscopy of the as-synthesized materials is consistent with the poly-L-lysine retaining its secondary structure. Grand canonical Monte Carlo simulations were also performed to validate the interpretation of the experimental adsorption results. The experimental isotherms are consistent with simulated isotherms of cylindrical pores 1.3-1.7 nm in size, in good agreement with expected values. Our results suggest a new avenue for synthesizing porous oxides with highly tuneable pore sizes and shapes under mild conditions.