The main factors affecting the porosity of methacrylate-ester based monolithic columns were investigated. We prepared 23 monolithic capillary columns with porosity controlled by varying the proportions of butyl methacrylate and ethylene dimethacrylate monomers and of 1,4-butanediol and 1-propanol as the porogen solvent in the polymerization mixtures by thermally initiated in-situ polymerization in fused-silica capillaries. Using mixture design software, we systematically varied the composition of the polymerisation mixtures to find significant factors affecting flow-through pore formation. Multivariate analysis of the experimental data obtained for the fabricated columns yielded a model for prediction of the flow-through porosity in monolithic beds as a function of the composition of the polymerization mixture used to prepare polymethacrylate monolithic capillary columns. The mean error of prediction was lower than 8% for eight columns prepared independently of the original set of 15 columns used to derive the flow-through model. The flow-through porosity increases with increasing concentration of the binary porogen solvent mixture, the concentration of 1,4-butanediol being the main factor enhancing flow-through pore formation. On the other hand, increasing concentrations of the hydrophobic monomer butyl methacrylate and increasing concentrations of 1-propanol have a negative effect on flow-through pore formation. The capillary columns prepared with a high proportion of flow-through pores and a minimum amount of mesopores can be used for fast gradient separations of both low-molecular weight compounds and biopolymers.