The first building blocks of life could be produced in ultramafic-hosted hydrothermal systems considering the large amounts of hydrogen and methane generated by serpentinisation and Fischer–Tropsch-Type synthesis, respectively, in those systems. The purpose of this study was to detect and characterise organic molecules in hydrothermal fluids from ultramafic-hosted hydrothermal systems in the Mid-Atlantic Ridge (MAR) region. During the EXOMAR cruise 2005, fluids from the Rainbow (36°14′N) and the Lost City (30°N) hydrothermal fields were collected and treated by Stir Bar Sorptive Extraction (SBSE) and Solid Phase Extraction (SPE). The extracts were analysed by Thermal Desorption–Gas Chromatography–Mass Spectrometry (TD–GC–MS) and GC–MS, respectively. Compared to nearby deep seawater, hydrothermal fluids were clearly enriched in organic compounds, with a more diverse spectrum of molecules. We observed a very similar range of organic compounds in fluids from both sites, with a dominance of aliphatic hydrocarbons (C9–C14), aromatic compounds (C6–C16) and carboxylic acids (C8–C18). The occurrence of these compounds is supported by other field studies on serpentinites and sulfide deposits. Literature on thermodynamic data and experimental work has suggested the possible abiogenic origin of hydrocarbons and organic acids. In addition, it has been shown elsewhere that catalytic reactions producing hydrocarbons likely occur at both Lost City and Rainbow hydrothermal fields as suggested by the evolution of δ13C with increasing C number for methane, ethane, propane and butane. In order to investigate the origin of the organic molecules in the fluids, compound-specific carbon isotope ratio measurements were performed on n-alkanes and carboxylic acids, for which the δ13C values were in the range of − 46 to − 20‰ (vs. V-PDB). These preliminary data did not allow conclusive support or rejection of an abiogenic origin of the compounds. Indeed, predicting δ13C signatures in hydrothermal systems is likely to be complicated, due to differences in source δ13C signatures (i.e., of the C building blocks), and a variety of, mostly unknown, fractionation steps which may occur along the synthesis pathways. In addition, even though a fraction of the compounds detected in the fluids is likely abiotically produced, a dominance of biogenic sources and/or processes might hide their characteristic signature.