A miniaturised method developed to measure the mineralisation of C-13-labelled organic compounds in small soil samples is presented. Soil samples (<0.5 g) were placed in wells of microtiter plates with CO2 traps (NaOH-soaked glass microfiber filters) and amended with C-13-labelled-labelled substrate. The microtiter plate was covered with a seal and placed in a microplate clamp system to ensure that each well was airtight. After incubation, the CO2 traps were transferred to tightly sealed glass phials under CO2-free atmosphere and the C-13-labelled-labelled CO2 was released by addition of H3PO4. The CO2 was measured by micro-GC and its isotopic signature was determined using a GC-IRMS. The qualitative and quantitative efficiency of the microplate system was demonstrated by comparison with direct measurement of CO2 in the headspace of phials in which similarly treated soil samples had been incubated. The two methods showed similar mineralisation rates for added C-13-labelled-substrates but the apparent mineralisation of soil organic matter was greater with the microtiter plate method. The microplate system presented here is suitable for studying the mineralisation of different kinds of C-13-labelled-labelled substrates in small soil samples and allows analysis of functional and molecular characteristics on the same micro-samples.