The (12)CO2/(13)CO2 isotope ratio is a well-known marker in breath for a variety of biochemical processes and enables monitoring, e.g., of the glucose metabolism during sepsis. Using animal models-here, at a mouse intensive care unit-the simultaneous determination of (12)CO2 and (13)CO2 within small volumes of mouse breath was enabled by coupling a novel low-volume hollow waveguide gas cell to a compact Fourier transform infrared spectrometer combined with multivariate data evaluation based on partial least squares regression along with optimized data preprocessing routines.