Fecundity is probably the most frequently studied fitness component in Drosophila. Nevertheless, currently used methods to measure fecundity are not well-suited for large-scale experiments, with many populations being assayed in parallel. Here we present a standardized pipeline to measure fecundity in many Drosophila population samples with substantially reduced hand on times. Using a high-contrast medium for egg laying, we developed a Java plug-in for ImageJ to quantify the number of eggs by image processing. We show that our method is fast and provides reliable egg counts.