•Laboratory experiments in simulated flight conditions for the analysis of chlorohydrocarons on Mars.•Separation and identification of chlorohydrocarbons with the SAM instrument onboard NASA’s Curiosity rover.•Elution of chlorohydrocarbons with various stationary phases. The Sample Analysis at Mars (SAM) instrument is a gas chromatograph-mass spectrometer onboard the NASA Curiosity rover, currently operating on the surface of Mars. Organic compounds are of major importance with regard to questions of habitability and the potential presence of life on Mars, and one of the mission’s main objectives is to analyze the organic content of soil and rock samples. In SAM’s first chromatographic measurements, however, unexpected chlorine-bearing organic molecules were detected. These molecules have different origins but the presence of perchlorates and chlorates detected at the surface of Mars suggests that reactivity between organic molecules and thermal decomposition products from oxychlorines is one of the major sources of the chlorinated organic molecules. Here we perform a comprehensive and systematic study of the separation of volatile chlorohydrocarbons with the chromatographic columns used in the SAM instrument. Despite the constrained operating conditions of the flight instrument, we demonstrate that SAM’s capillary chromatographic columns allow for effective separation and identification of a wide range of chlorine-bearing species. We also show that instrumental limitations prevent the detection of certain molecules, obscuring our ability to make definitive conclusions about the origin of these organic materials.