Analysis of the propagation of measurement error into a computed quantity such as building aerial emissions provides insight into which measurements should be improved. An analysis of different instrument measurements, sampling period, and different sites all together comprise an objective means of determining optimal sampling strategies. This paper describes the measurement system uncertainty analysis useful for emissions research, and how it can lead to design and project improvements to obtain emissions estimates with statistical confidence. This study is an analysis of the Kentucky broiler house study as part of the US EPA Air Consent Agreement, and was used to develop a category I Quality Assurance Project Plan. Results of the analysis suggest that the standard uncertainty in ammonia emission from broiler houses in the study was typically under 10%, and increased with uncertainty in ventilation rate, but decreased as ventilation rate increased. The uncertainty is quantified for normal conditions and for conditions in which the instrumentation is at the calibration threshold.