Zwitterionic methacrylate based polymeric monolithic columns were prepared in two-step polymerizations, with reduced polymerization times. Characteristic properties such as hydrodynamic permeability, porosity, retention factors, and pore size distribution charts were used for column evaluation. A scaffold column was fabricated by polymerization of poly(lauryl methacrylate-co-tetraethyleneglycol dimethacrylate) and was used without further modification as a support for a poly(N,N-dimethyl-N-methacryloxyethyl-N-(3-sulfopropyl)ammonium betaine-co-bisphenol A glycerolate dimethacrylate) second monolith layer with zwitterionic functionality, for HILIC separations. An additional internal structure was formed by the second monolithic layer. The fabrication procedure was reproducible with RSD<5%. Field emission scanning electron microscopy has also been used to investigate column pore morphology, using a novel technique where the polymeric material is imaged directly, without coverage with a conducting film or particles. The new polar monolithic columns were used for HILIC separations of phenolic acids, flavones, nucleosides, and bases of nucleic acids, with similar efficiencies but different selectivities for zwitterionic methacrylate monolithic columns recently prepared by single step polymerization.