Semiconductor structures used for fundamental or device applications most often incorporate alloy materials. In “usual” or “common” III–V alloys, based on the InGaAsP or InGaAlAs material systems, the effects of compositional disorder on the electronic properties can be treated in a perturbative approach. This is not the case in the more recent nitride-based GaInAlN alloys, where the potential changes associated with the various atoms induce strong localization effects, which cannot be described perturbatively. Since the early studies of these materials and devices, disorder effects have indeed been identified to play a major role in their properties. Although many studies have been performed on the structural characterization of materials, on intrinsic electronic localization properties, and on the impact of disorder on device operation, there are still many open questions on all these topics. Taking disorder into account also leads to unmanageable problems in simulations. As a prerequisite to address material and device simulations, a critical examination of experiments must be considered to ensure that one measures intrinsic parameters as these materials are difficult to grow with low defect densities. A specific property of nitride semiconductors that can obscure intrinsic properties is the strong spontaneous and piezoelectric fields. We outline in this review the remaining challenges faced when attempting to fully describe nitride-based material systems, taking the examples of LEDs. The objectives of a better understanding of disorder phenomena are to explain the hidden phenomena often forcing one to use ad hoc parameters, or additional poorly defined concepts, to make simulations agree with experiments. Finally, we describe a novel simulation tool based on a mathematical breakthrough to solve the Schrödinger equation in disordered potentials that facilitates 3D simulations that include alloy disorder.