Large-scale laboratory experiments often necessitate the processing of numerous samples in little time, their long-time storage and the joint analysis of morphological, biochemical, and microbiological features. Combining different types of assays is often not compatible with classical methods to estimate size in adult Drosophila flies. We therefore designed a new spectrophotometric assay for the high-throughput estimation of adult size in Drosophila that facilitates microbial and biochemical content analysis. The new method uses optical density at 202 nm of single fly homogeneates as size proxy. We tested the method in a variety of Drosophila populations -including wild caught flies- and compared its explanatory power with two classical size estimates: wet-weight and wing-length. It was also used to control for size when comparing the fat content of different fly populations. Results show fly homogenate optical density is an powerful size proxy that may be used for both male and female flies.