Organofluorine substances are found in a wide range of materials and solvents commonly used in industry and homes, as well as pharmaceuticals and pesticides. In the environment, organofluorine molecules are now recognized as an important class of anthropogenic pollutants. Fingerprinting organofluorine compounds via their carbon isotope ratios ( 13 C/ 12 C) is crucial for correlating molecules with their source. Here we apply a 19 F nuclear magnetic resonance spectroscopy (NMR) technique to obtain the first position-specific carbon isotope ratios for a diverse set of organofluorine molecules. In contrast to traditional isotope ratio mass spectrometry, the 19 F NMR method provides 13 C/ 12 C isotope ratios at each carbon position where a C−F bond is present, and does not require fragmentation or combustion to CO 2 , overcoming challenges posed by the robust C−F covalent bonds. The method was validated with 2,2,2-trifluoroethanol, and applied to analyze heptafluorobutanoic acid, 5-fluorouracil and fipronil. Results reveal distinct intramolecular carbon isotope distributions, enabling differentiation of chemically identical molecules. Notably, the NMR method accurately analyzes carbon isotopes within target molecules despite impurities. Potential applications include the detection of counterfeit products and drugs, and ultimately pollution tracking in the environment.