In this thesis we consider inverse problems involving multiscale elliptic partial differential equations. The name multiscale indicates that these models are characterized by the presence of parameters which vary on different spatial scales (macroscopic, microscopic, mesoscopic, etc.). The variations at the smallest scales make these equations very difficult to approximate also when considering forward problems, since classical numerical methods require a mesh resolution at the finest scales, hence a computational cost that is often prohibitive. For this reason one prefers to apply homogenization or effective methods which, neglecting what happens at the smallest scales, are able to provide accurate macroscopic solutions to the problem. For what concerns the solution of inverse problems, we propose then a new numerical algorithm based on homogenization techniques, model order reduction and regularization methods. First, we consider elliptic operators whose tensor varies on a microscopic scale. Under the assumption that the nature of its micro structure is known, we aim at recovering a macroscopic parameterization of the tensor from measurements originating from the full multiscale model, using homogenization. Practical examples include multi-phase media whose constituents are known, but their respective volume fraction is unknown. We consider the Calderón's formulation of the inverse problem. We prove that, under some regularity assumptions on the fine scale tensor, the effective inverse problem, with observed data consisting of the homogenized Dirichlet to Neumann (DtN) map, is also well-posed. We then solve the problem by considering finite measurements of the multiscale DtN map and using Tikhonov regularization, and we establish a convergence result of the solution by means of G-convergence. In a second stage, we consider a Bayesian approach which allows for uncertainty quantification of the results. We prove existence and well-posedness of the effective posterior probability measure, obtained by homogenization of the observation operator. By means of G-convergence we characterize the discrepancy between the fine scale and the homogenized model, and we prove convergence of the effective posterior towards the fine scale posterior in terms of the Hellinger distance. We also propose a numerical procedure to estimate the homogenization error statistics, which, if included in the inversion process, allow to account for approximation errors. Finally, we deal with multiscale inverse problems for the linear elasticity equation. In this context we assume that the heterogeneity of the material is determined by its geometry rather than by the coefficients of the equation. In particular, we consider porous media with random perforations and, following the Bayesian approach, we solve the inverse problem of determining the elastic properties of an hypothetical isotropic material. We prove the existence and well-posedness of the effective posterior measure, as well as its convergence in the fine scale limit by means of G-convergence. We conclude by describing a new probabilistic numerical method which computes a new posterior measure that accounts for approximation errors and reveals the uncertainty intrinsic in the numerical method.