The mechanistic pathway taken in constructing a three-dimensional polymer network was greatly influenced by the reactivity and the functionality of the monomers and cross-linkers used. An increase in the cross-linker reactivity and functionality were found to promote properties in the polymer network that are consistent with a microgel type polymer structure. The microstructure of polyacrylamide (PAAm) gels synthesized from acrylamide (AAm) with a variety of cross-linkers was investigated using temperature profiles and polymerization rates, electrophoresis, scanning electron microscopy, and clarity tests. It was discovered that the heterogeneity of these polymers is largely due to the increased reactivity of the cross-linkers and ultimately responsible for improved properties of PAAm gels such as optical clarity and enhancement of electrophoretic separation.