This paper deals with the problem of robust output synchronization for heterogeneous multi-agent systems. First, a new synchronization approach is presented to synchronize the outputs of heterogeneous agents. Based on noninteracting control techniques, a method is derived for homogenizing the input-output behavior of every agent. Hence, applying the same reference input signal to every agent leads to synchronization. Furthermore, a strategy for increasing the robustness of the synchronization process against exogenous disturbances is presented, which leads to a structurally constrained optimization problem. However, by a convenient reformulation of the problem, well established tools from robust control theory can be used. Moreover, it is shown that this procedure allows to separate the robustness issue from the synchronization task. The effectiveness of the approach is illustrated by a robust output synchronization example for a heterogeneous aircraft fleet.