We report the room temperature formation of aminated mesoporous silica nanoparticles (NH 2-MSNs) by means of co-condensation of different molar ratios of tetraethyl orthosilicate (TEOS) and 3-aminopropyl triethoxysilane (APTES) in the synthesis feed. The resulting materials are characterized by a combination of transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), Fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), and N 2 adsorption/desorption measurements. Analysis reveals that an increase in APTES loading (mol %) leads to structural transitions in the MSNs from hexagonal (0-49 mol %) to cubic Pm3̄n (54-64 mol %) to disordered at very high APTES amounts (69 mol %). Investigation of structural evolution during cubic Pm3̄n particle synthesis reveals early particle formation stages that are surprisingly similar to those discussed in recent literature on nonclassical single crystal growth. These include significant heterogeneities in particle density despite crystallographic orientation across the entire particle as well as particle growth via addition of preformed and prestructured silica clusters. Syntheses at varying pH reveal further details of the structure formation process. The results pose fundamental questions about the relation between formation mechanisms of classical crystalline materials and mesoscopically ordered, locally amorphous materials. © 2012 American Chemical Society.