1. Improved understanding of the carbon (C) cycle is essential to model future climates and how this may feedback to affect greenhouse-gas fluxes. 2 .We summarize previous work quantifying respiration rates of organic substrates and briefly discuss how advances in technology, specifically the use of chambers linked to a non-dispersive infra-red gas analyzer (NDIR), can be applied to assess carbon dynamics from short-term field measurements. This technology hastens measurement and is relatively inexpensive, enabling researchers to increase replication and investigate temporal and spatial variation. 3. We describe the theory behind calculations of CO2 efflux released through organic substrates, when using a closed-chamber linked to a NDIR. These methods can in principle be extended to any chamber-based measurement of gas fluxes, including partially closed chambers as used for soil surface CO2, nitrous oxide or methane effluxes and stem CO2 respiration, although additional assumptions may apply. 4. We show that incorrect application of formulae in some earlier studies resulted in either under- or over-estimation of CO2 effluxes. Of the studies we reviewed measuring the respiration of woody debris, leaf-litter, or woody stems using closed chambers linked to a NDIR, only 22% (11 of 51) provided the equations used to calculate CO2 efflux, and 72% (8 of 11) of those provided contained basic errors. Using our data on the decomposition of woody debris as an example, we found that such mistakes resulted in anywhere from 8% underestimation to 22% overestimation of CO2 efflux. The errors varied among studies and hence may limit understanding of the factors affecting emissions of CO2 and our ability to incorporate this knowledge into global carbon models. 5. We provide formulae for the correct calculation of respiration rates in future studies using closed-chambers and thus provide a basis for comparative studies of factors affecting CO2 efflux from woody debris, leaf litter and other substrates. Ultimately this will contribute to improved parameterization of forest respiration.