In this paper, a new distributed model reference adaptive control (MRAC) design framework is proposed for containment control of heterogeneous uncertain multi-agent systems (MAS). Both groups of leaders and followers are considered to have general linear dynamics with the leaders subject to bounded external inputs and the followers subject to uncertain system dynamics. A novel distributed adaptive control protocol is developed under this new framework, which incorporates robust adaptive control with nonlinear compensator techniques to cope with unmeasurable bounded leaders' inputs and uncertain agent dynamics. Convergence of the containment control errors to an arbitrarily adjustable neighborhood of the origin is guaranteed based on the Lyapunov method. The proposed MRAC framework provides a promising alternative solution over the prevailing cooperative output regulation framework for heterogeneous linear MAS containment control. It enables us to handle more general system settings under more stringent control environments with limited accessibility of leaders' information and uncertain follower dynamics.