Transparent CdSe(ZnS) sol-gel materials have potential uses in optoelectronic applications such as light emitting diodes (LEDs) due to their strong luminescence properties and the potential for charge transport through the prewired nanocrystal (NC) network of the gel. However, typical syntheses of metal chalcogenide gels yield materials with poor transparency. In this work, the mechanism and kinetics of aggregation of two sizes of CdSe(ZnS) core(shell) NCs, initiated by removal of surface thiolate ligands using tetranitromethane (TNM) as an oxidant, were studied by means of time-resolved dynamic light scattering (TRDLS); the characteristics of the resultant gels were probed by optical absorption, transmission electron microscopy (TEM) and small angle X-ray scattering (SAXS). At low concentrations of NCs (ca. 4 × 10(-7) M), the smaller, green-emitting NCs aggregate faster than the larger, orange-emitting NCs, for a specific oxidant concentration. The kinetics of aggregation have a significant impact on the macroscopic properties (i.e. transparency) of the resultant gels, with the transparency of the gels decreasing with the increase of oxidant concentration due the formation of larger clusters at the gel point and a shift away from a reaction limited cluster aggregation (RLCA) mechanism. This is further confirmed by the analyses of the gel structures by SAXS and TEM. Likewise, the larger orange-emitting particles also produce larger aggregates at the gel point, leading to lower transparency. The ability to control the transparency of chalcogenide gels will enable their properties to be tuned in order to address application-specific needs in optoelectronics.