A method for the quantitative determination of seven pharmaceuticals in bivalves was developed by QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) extraction, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) with electrospray ionization. Both the European Standard Method EN 15662 and the AOAC Official Method 2007.01 for QuEChERS were tested. In addition, several clean-up strategies were evaluated in order to clean the matrix previous to the LC-MS/MS analyses. Dispersive solid-phase extraction with silica gel and modification of the chromatographic separation were the clean-up strategies that gave the best results. The optimized method was validated in mussels (Mytilus galloprovincialis) and allowed the determination of pharmaceuticals at nanograms per gram levels (dry weight (d.w.)). Limits of quantification ranged from 5 to 100 ng/g. Apparent recoveries ranged from 35 to 77%. The application of this method to bivalves revealed the presence of salicylic acid at concentrations up to 103 ng/g (d.w.).