AbstractProtein antigens encapsulated as vaccines in poly[(rac-lactide)-co-glycolide] (PLGA) microparticle carriers can induce immune responses. The intensity and directions of this response can be controlled by coloading the microparticles with immunomodulatory adjuvants, e.g., muramyl dipeptide (MDP) as adjuvant combined with ovalbumin (Ova) as protein antigen. In this study, methodologies for an individual quantification of both encapsulated substances should be reported, which comprise (i) a separation process to isolate and determine MDP as intact molecule and (ii) a simultaneous degradation of both analytes with subsequent specific quantification of Ova fragments. It was shown that coloading of both substances resulted in a substantially reduced encapsulation efficiency of MDP. This illustrates that correct conclusions on dose–response relationships in future vaccination studies can only be drawn, if a selective method for adjuvant and protein quantification will be applied.