Recent data suggest that small differences in editing efficiency can have significant functional consequences. Here we present a fluorescent poisoned primer extension assay that is capable of distinguishing editing efficiency differences as low as 5%. For a poison-primer extension assay to be accurate, the extension product must stop at the intended base. Sometimes, however, it runs beyond. We tested the effect of specific enzyme-terminator combinations on the amount of run through. In the worst cases it accounted for 70% of the total signal, and in the best cases <5%. In addition, the specific base can affect run through, with G producing the least. The accuracy of the assay was demonstrated on templates derived from mixed plasmids and then verified on two biological substrates. Using either a K(+) channel mRNA that contains a site for adenosine deamination or an ndhB mRNA that contains a site for cytidine deamination, the editing efficiency predicted by the assay closely matched that predicted by bulk sequencing of individual cDNA clones. This assay should prove useful for analyzing small changes in editing efficiency or for quantifying single nucleotide polymorphisms.