This monograph provides a more unified and self-contained presentation of the results presented in Popa's earlier papers on this topic. The classification is in terms of the standard invariant $\mathcal G_{\mathcal N,\mathcal M} $ of the subfactor $\mathcal N\subset \mathcal M$. This invariant is a lattice of inclusions of finite dimensional algebras associated with the Jones iterated basic construction for $\mathcal N\subset \mathcal M$. ""Classification of Subfactors and Their Endomorphisms"" is based on lectures presented by Popa at the NSF-CBMS Regional Conference held in Eugene, Oregon, in August 1993.