This paper addresses the effect of microstructure uncertainties on elastic properties of nanocomposites using finite element analysis (FEA) simulations. Computer-simulated microstructures were generated to reflect the variability observed in nanocomposite microstructures. The effect of waviness, agglomeration, and orientation of carbon nanotubes (CNTs) were investigated. Generated microstructures were converted to image-based 2D FEA models. Two hundred different realizations of microstructures were generated for each microstructure type to capture the stochastic response. The results confirm previously reported findings and experimental results. The results show that for a given fiber volume fraction, CNTs orientation, waviness, and agglomeration result in different elastic properties. It was shown that while a given microstructural feature will improve the elastic property, it will increase the variability in the elastic properties.