Liquid chromatography/mass spectrometry (LC/MS) and capillary electrophoresis/mass spectrometry (CE/MS) assume a central role in pharmaceutical research. Both experimental arrangements are routinely used in various pharmaceutical laboratories to provide solutions to a wide range of problems including purity testing, identification and structural elucidation of metabolites, monitoring of biological and toxicological tests and confirmation of newly synthesized chemical identities and their potential synthetic and/or degradation impurities. Over the last few years an exponential increase in the use of both methods to tackle diverse and challenging pharmaceutical tasks has been witnessed. Such an impressive increase has its roots in the capability of both analytical methods to provide information on retention (migration) times: molecular masses and fragmentation pathways in a single run of analysis. In the present article a number of representative examples on the application of both techniques in pharmaceutical research and process control are discussed.