Methane emission is an important tool in the evaluation of manure management systems due to the potential impact it has on global climate change. Field procedures used for estimating methane emission rates require expensive equipment, are time consuming, and highly variable between farms. The purpose of this paper is to report a simple laboratory procedure for estimating methane emission from stored manure. The test developed was termed a methane production rate (MPR) assay as it provides a short-term biogas production measurement. The MPR assay incubation time is short (3d), requires no sample preparation in terms of inoculation or dilution of manure, is incubated at room temperature, and the manure is kept stationary. These conditions allow for high throughput of samples and were chosen to replicate the conditions within deep-pit manure storages. In brief, an unaltered aliquot of manure was incubated at room temperature for a three-days to assay the current rate of methane being generated by the manure. The results from this assay predict an average methane emission factor of 12.2 ± 8.1 kg CH4 head−1 yr−1 per year, or about 5.5 ± 3.7 kg CH4 per finished animal, both of which compare well to literature values of 5.5 ± 1.1 kg CH4 per finished pig for deep-pit systems (Liu et al., 2013). The average methane flux across all sites and months was estimated to be 22 ± 17 mg CH4 m−2-min−1, which is within literature values for deep-pit systems ranging from 0.24 to 63 mg CH4 m−2-min−1 (Park et al., 2006) and similar to the 15 mg CH4 m−2-min−1 estimated by (Zahn et al., 2001).