In grassland ecosystems, soil animals act as key soil engineers and architects. The diversity of soil animals is also a regulator of ecosystem carbon flow. However, our understanding of the link between soil animals, carbon fluxes and soil physical organisation remains poor. An integrated approach based on soil micromorphology and laser ablation stable isotope ratio mass spectrometry (LA-IRMS) was developed to provide spatially distributed data of pulse-derived 13C tracer from roots in the soil environment. This paper describes the development and testing of a LA-IRMS 13C/12C analytical method on soil thin sections as a means to determine the fate of root carbon derived from photosynthesis into soil. Results from this work demonstrated (1) that micro-scale δ13C (‰) analysis could be made on targeted features located within a soil thin section and (2) that LA-IRMS δ13C (‰) measurements made on samples obtained from 13CO2 pulse labelled plant-soil blocks confirmed the presence of recent photosynthates in the rhizosphere (1 and 4 weeks post-pulse). Copyright © 2002 John Wiley & Sons, Ltd.