Mesoporous silica particles are of significant interest for biomedical applications due to their good general biocompatibility compared to other nanoparticle matrices such as quantum dots, high specific surface areas up to 1000 m2/g, and extreme synthetic tunability in terms of particle size, pore size and topology, core material, and surface functionalization. For one application, drug delivery, mesoporous silica nanoparticles (MSNs) of two pore structures, MCM-41 – parallel, hexagonally ordered pores approximately 3 nm in diameter – and wormhole (WO) – interconnected, disordered pores also approximately 3 nm in diameter – were synthesized with particle diameters under 100 nm. Additionally, a magnetic Fe3O4 nanoparticle core was incorporated into Fe3O4-core WO-MS-shell particles. The particles were loaded with doxorubicin, a chemotherapeutic, and the drug release into phosphate buffered saline (PBS, 10 mM, pH 7.4) at 37 °C was monitored by fluorescence spectroscopy. The data were fit to three models: Korsmeyer-Peppas, first order exponential release, and Weibull. The Korsmeyer-Peppas model provided useful information concerning the kinetics and mechanism of drug release from each MSN type. A small but statistically significant difference in the release kinetics was found due to the different pore topologies. A much larger kinetic effect was observed due to the inclusion of an iron oxide core. Applying a static magnetic field to the Fe3O4-core WO-MS shell particles did not have a significant impact on the doxorubicin release. This is the first time that the effects of pore topology and iron oxide core have been isolated from pore diameter and particle size for these materials. In vitro cell studies were conducted to determine the cytotoxicity of the bare and doxorubicin-loaded materials against three cancerous cell lines – A549 human lung carcinoma cells, HEC50CO human endometrial cancer cells, and CT26 mouse colon cancer cells. The MCM-41 and WO MSNs generally displayed similar toxicities within each cell line, and the Fe3O4-core WO-MS shell particles were less toxic. Doxorubicin-loaded particles generally displayed greater toxicity than bare MSNs, but the A549 cells were very resistant to all concentrations of MSNs tested. For another biomedical application, tissue phantom development, mesoporous silica particles with approximately 10 μm diameters and C18 surface functionalization were evaluated for their use as a substrate for optical tissue phantoms. Tissue phantoms are synthetic imitations of biological material, and C18-modified silica provides a substrate that is simple to load with optically active biological molecules. The molecules are then hydrophobically trapped to maintain a clear optical boundary between the biological loading within the particle and an aqueous suspension gel. Several preparation techniques were evaluated for the dispersal of hydrophobic particles in aqueous media, and qualitative analysis indicated that surfactant coating of the outer surface could fully disperse the hydrophobic particle while maintaining the clear optical boundary. A novel analysis was developed to provide a single numerical indicator of clustering for a quantitative assessment of particle dispersal in tissue phantoms.