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We provide a general framework for self-interacting warm dark matter (WDM) in cosmological perturbations, by deriving from first principles a Boltzmann hierarchy which retains certain independence from a particular interaction Lagrangian. We consider elastic interactions among the massive particles, and obtain a hierarchy which is more general than the ones usually obtained for non-relativistic (as for cold DM) or for ultra-relativistic (as for neutrinos) approximations. The more general momentum-dependent kernel integrals in the Boltzmann collision terms, are explicitly calculated for different field-mediator models, including examples of a scalar field (either massive or massless) or a massive vector field. As an application, we study the evolution of the interaction rate per particle under the relaxation time approximation, and assess when a given self-interaction is relevant in comparison with the Hubble expansion rate. Our framework aims to be a useful starting point to evaluate DM self-interaction effects in the linear power spectrum, necessary to then study its evolution all the way to non-linear stages of structure formation, where certain DM interactions were proven to be relevant.