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The French National Radioactive Waste Management Agency (ANDRA) has recently developed a new experimental set-up which allows sampling water from marl rock formations, together with an in situ characterisation of the composition and migration mechanisms of the gases dissolved in the marl porewater. Gases and liquids are collected from vertical borehole drillings in underground laboratories. The analytical design, Fourier transformed infrared spectroscopy based, allows powerful and long term on-line monitoring of gases released by low-permeability media. The IR system is designed to cope with the unfavourable measurement conditions occurring in an experimental underground laboratory (moisture, dust, etc.). Because the working conditions in such an underground laboratory make complete purging of the IR spectrometer difficult, the IR spectra of geological gases are often perturbed by contributions from atmospheric CO 2 and water vapour. The metrology aspect is based on an IR low resolution sensor equipped with two measurement compartments. In the internal compartment linked to the borehole layout, gases are monitored on-line through a cell with a variable optical path, whereas in the external compartment, atmospheric CO 2 is measured through a short open path configuration. The experimental method and data processing procedure used to determine the real partial pressure of CO 2 arising from the marl rock formation are described in this paper. Results of the on-line gas (CO 2 and CH 4 ) monitoring conducted in the Mont Terri underground laboratory are presented and compared with punctual gas chromatography analyses.