Compound-specific isotope analysis (CISA) of non-volatile analytes has been enabled by the introduction of the first commercial interface to hyphenate liquid chromatography with an isotope ratio mass spectrometer (LC-IRMS) in 2004, yet carbon isotope analysis of unpolar and moderately polar compounds is still a challenging task since only water as the eluent and no organic modifiers can be used to drive the separation in LC. The only way to increase the elution strength of aqueous eluents in reversed phase LC is the application of high temperatures to the mobile and stationary phases (HT-LC-IRMS). In this context we present the first method to determine carbon isotope ratios of pharmaceuticals that cannot be separated by already existing separation techniques for LC-IRMS, such as reversed phase chromatography at normal temperatures, ion-chromatography, and mixed mode chomatography. The pharmaceutical group of sulfonamides, which is generally mixed with trimethoprim in pharmaceutical products, has been chosen as probe compounds. Substance amounts as low as 0.3 μg are sufficient to perform a precise analysis. The successful applicability and reproducibility of this method is shown by the analysis of real pharmaceutical samples. The method provides the first tool to study the pharmaceutical authenticity as well as degradation and mobility of such substances in the environment by using the stable isotopic signature of these compounds.