We present an algorithm for the generation of optimal trajectories for teams of heterogeneous quadrotors in three-dimensional environments with obstacles. We formulate the problem using mixed-integer quadratic programs (MIQPs) where the integer constraints are used to enforce collision avoidance. The method allows for different sizes, capabilities, and varying dynamic effects between different quadrotors. Experimental results illustrate the method applied to teams of up to four quadrotors ranging from 65 to 962 grams and 21 to 67 cm in width following trajectories in three-dimensional environments with obstacles with accelerations approaching 1g.