Multi-residue analytical methodologies are becoming the preferred and required tools against single group analysis, as they provide wider knowledge about the occurrence of pharmaceuticals in the environment necessary for further study of their removal, partition and ultimate fate. However, simultaneous analysis of compounds from different groups with quite different physico-chemical characteristics requires a compromise in the selection of experimental conditions, which in some cases are not the best conditions for all the analytes studied. In this article, an overview of analytical methodologies focusing on the simultaneous determination of acidic, neutral and basic compounds belonging to different therapeutical classes is presented. The state-of-the-art of LC-MS/MS for multi-class analysis is reviewed, highlighting the specific requirements for such analysis.