Mesoporous aggregates of nanocrystalline zeolites with MFI and BEA frameworks have been synthesized using a one-pot and single structure directing agent. The effect of different reaction conditions, such as temperature, time, pH and water content, on the particle size, surface area and mesopore volume has been studied. Nanocrystalline and mesoporous ZSM-5, β and Y zeolites were modified with different transition metals and the resulting single-and double metal containing catalyst materials were characterized. Nanocrystalline Silicalite-1 zeolite samples with varying particle size were functionalized with different organosilane groups and the cytotoxic activity of the zeolite nanocrystals was studied as a function of particle size, concentration, organic functional group type, as well as the type of cell line. Framework stability of nanocrystalline NaY zeolite was tested under different pH conditions. The synthesized zeolites used in this work were characterized using a variety of physico-chemical methods, including powder X-ray diffraction, Solid State NMR, nitrogen sorption, electron microscopy, Inductively Coupled Plasma-Optical Emission Spectroscopy and X-ray Photoelectron Spectroscopy.