Most existing Multiple-Instance Learning (MIL) algorithms assume data instances and/or data bags are independently and identically distributed. But there often exists rich additional dependency/structure information between instances/bags within many applications of MIL. Ignoring this structure information limits the performance of existing MIL algorithms. This paper explores the research problem as multiple instance learning on structured data (MILSD) and formulates a novel framework that considers additional structure information. In particular, an effective and efficient optimization algorithm has been proposed to solve the original non-convex optimization problem by using a combination of Concave-Convex Constraint Programming (CCCP) method and an adapted Cutting Plane method, which deals with two sets of constraints caused by learning on instances within individual bags and learning on structured data. Our method has the nice convergence property, with specified precision on each set of constraints. Experimental results on three different applications, i.e., webpage classification, market targeting, and protein fold identification, clearly demonstrate the advantages of the proposed method over state-of-the-art methods.