Polymerization in lyotropic liquid crystalline (LLC) media is a promising method enabling synthesis of nanostructured organic polymers. To understand polymer structure development in LLC systems, this study investigates the polymerization of acrylate monomers of differing polarity and size within the hexagonal and lamellar phase of dodecyltrimethylammonium bromide and water. LLC structure, polymer morphology, and polymerization behavior were characterized to understand the connection between polymerization environment and formation of polymer structure. While the order of the template phase highly influences final polymer order, variations in monomer chemistry can lead to significantly different polymer structures even from the same liquid crystalline phase. More rapid polymerization, which leads to higher conversion and higher cross-link density of the relatively low molecular weight monomers, yields highly anisotropic polymer structure exhibiting alignment of 800 nm channels extending for lengths greater than 150 mu m. Less ordered polymer structure results with analogous monomers of higher molecular weight. While polymer structure appears to result from a phase separation process in these systems, the structure directing influence of the liquid crystalline media is exhibited in several systems including the formation of highly oriented cylindrical structures with diameter of 200 nm from polymerization of poly(ethylene glycol) dimethacrylate in the hexagonal phase. Significant control of polymer structure has been demonstrated using LLC templates through proper selection of monomer chemistry, concentration, and LLC template structure.