Reductions in measurement uncertainty for organic micro-pollutant concentrations in full scale compost piles using comprehensive sampling and allowing equilibration time before sampling were quantified. Results showed that both application of a comprehensive sampling procedure (involving sample crushing) and allowing one week of equilibration time before sampling reduces measurement uncertainty by about 50%. Results further showed that for measurements carried out on samples collected using a comprehensive procedure, measurement uncertainty was associated exclusively with the analytic methods applied. Application of statistical analyses confirmed that these results were significant at the 95% confidence level. Overall implications of these results are (1) that it is possible to eliminate uncertainty associated with material inhomogeneity and (2) that in order to reduce uncertainty, sampling procedure is very important early in the composting process but less so later in the process.