We present a method for the rapid and accurate quantitative analysis of paraquat (PQ) in biological samples. Paraquat, also known as methyl viologen, is commonly used to induce oxidative stress in laboratory studies. Our method uses classical standard addition methodology and ultra-high performance liquid chromatography (UPLC) with photodiode array detection to estimate recovered PQ in whole-organism homogenates. The method facilitates simple and accurate quantification of PQ present in a biological sample, a much more biologically meaningful parameter than the dose of PQ administered in an experimental treatment. In an example using 4 different genotypes of Drosophila melanogaster exposed to 10 mM PQ, we measured concentrations from 2.8 to 6.3 μM, corresponding to 1.2 to 2.6 × 10−12 mol PQ per mg of fly. Analysis is simple, uses minimal sample preparation, and exploits the resolution and speed of UPLC to provide rapid (3 min) assays of homogenate samples.