We present the relativistic calculation of the hyperfine structure in pionic and kaonic atoms. A perturbation method has been applied to the Klein-Gordon equation to take into account the relativistic corrections. The perturbation operator has been obtained \textit{via} a multipole expansion of the nuclear electromagnetic potential. The hyperfine structure of pionic and kaonic atoms provide an additional term in the quantum electrodynamics calculation of the energy transition of these systems. Such a correction is required for a recent measurement of the pion mass.