We describe an innovative platform for fully automated handling and observation of C. elegans, combined with dedicated software for data collection and analysis. Our microfluidic device allows, for the first time, automated high-content phenotyping of worms at medium/high-throughput, via accurate control and real-time monitoring of multiple physiological parameters in the worms. This screening format significantly minimizes the amount of compound needed for each test and could be readily used to identify toxicity mechanisms of substances, through specific phenotypic responses in the worms, within only 3 days. As a pilot study, we validated our platform by screening compounds with well-defined toxicity profiles. By monitoring larval growth, worm fertility and motility over 3 day-experiments, we successfully identified distinct patterns related to specific toxicity profiles of the tested compounds. In conclusion, we propose an innovative solution for rapid identification of toxic compounds and their potential mechanism of toxicity, using a biological model that perfectly bridges the gap between in vitro and in vivo assays.