A dual‐inlet isotope ratio mass spectrometer (VG‐SIRA 12, Isotech, Middlewich, England) using sealed‐glass combustion sample preparation and an automated single‐inlet isotope ratio mass spectrometry system (RoboPrep Sample Converter interfaced with a TracerMass Stable Isotope Detector, Europa Scientific, Crewe, England) were compared for δ13C analysis. Two hundred twenty four samples of plant and animal tissue were analyzed for S13C using the two systems. Delta13C values obtained from the two instruments were highly correlated (r2=0.986, P=0.0001). The slope of the relationship was not different from one nor was the Y‐intercept different from zero (Y=‐0.2 + 1.0X; P=0.86 and P=0.28 for the slope and Y‐intercept, respectively). In addition, samples from two complete experiments were run on both mass spectrometery systems and statistical analyses performed. In both experiments, differences between treatments were detectable using the RoboPrep system that were not detectable using the SIRA 12 system. In all cases mean δ13C values were comparable between the two systems, and coefficients of variation were low; well within acceptable experimental limits.