A multigrid technique for uniformly preconditioning linear systems arising from a mortar finite element discretization of second order elliptic boundary value problems is described and analyzed. These problems are posed on domains partitioned into subdomains, each of which is independently triangulated in a multilevel fashion. The multilevel mortar finite element spaces based on such triangulations (which need not align across subdomain interfaces) are in general not nested. Suitable grid transfer operators and smoothers are developed which lead to a variable Vcycle preconditioner resulting in a uniformly preconditioned algebraic system. Computational results illustrating the theory are also presented.