Nanostructured composite materials made of organic matrices and inorganic nanoparticles (NPs) represent the new paradigm of functional hybrid materials. This dissertation is focused on the synthesis and self-assembly of NPs within organic matrices which act as templates, targeting the formation of use-inspired structures. Particularly, self-assembly of macromolecules such as proteins and polymers, and polymer-functionalized NPs is utilized to create ordered assemblies of NPs. Inspired by the formation of chains of magnetic NPs in a group of bacteria referred to as Magnetotactic bacteria, we used Mms6, a biomineralization protein, as a template towards the formation of self-assembled arrays of magnetic NPs. Surface sensitive techniques such as atomic force microscopy, scanning electron microscopy and X-ray photoelectron spectroscopy, show the formation of these arrays on solid substrates. An alternative to the use of templates is to directly control the interactions between the NPs. In the presence of short dithiol tethers, gold nanoparticles crosslink covalently and form assemblies with short ranged FCC-like order. PEG functionalized nanoparticles, obtained by ligand exchange procedure, form a crystalline monolayer at the vapor-liquid interface in the presence of electrolytes in the suspension. In the presence of a complexing polymer (specifically, neutral PAA) the crystallinity of these monolayers decreases and NPs aggregate in the bulk. Analysis of these aggregates shows that in contrast to the covalent linkage, non-covalent interactions (hydrogen bonds and van der Waal's forces, via inter-polymer complexes) between the poly(ethylene glycol) (PEG) functionalized NPs, lead to the formation of FCC superlattices of NPs. Theoretical considerations of the variation of inter-particle distances show the significance of van der Waal's forces in these superlattices. Self-assembly processes used to create ordered assemblies of nanoparticles developed here are promising routes to fabricate functional nanomaterials such as metamaterials.