In this paper, we study the homogenization of a set of Smoluchowski's discrete diffusion-coagulation equations modeling the aggregation and diffusion of β-amyloid peptide (Aβ), a process associated with the development of Alzheimer's disease. In particular, we define a periodically perforated domain Ω ǫ , obtained by removing from the fixed domain Ω (the cerebral tissue) infinitely many small holes of size ǫ (the neurons), which support a non-homogeneous Neumann boundary condition describing the production of Aβ by the neuron membranes. Then, we prove that, when ǫ → 0, the solution of this micro-model two-scale converges to the solution of a macro-model asymptotically consistent with the original one. Indeed, the information given on the microscale by the non-homogeneous Neumann boundary condition is transferred into a source term appearing in the limiting (homogenized) equations. Furthermore, on the macroscale, the geometric structure of the perforated domain induces a correction in that the scalar diffusion coefficients defined at the microscale are replaced by tensorial quantities.