Background: The annotation or identification of small molecules during metabolomics studies is a difficult task that requires robustness in the process and reporting of the results and methods applied. The Critical Assessment of Small Molecule Identification (CASMI) contest was designed as a medium for researchers to exchange ideas and best practices related to how best to annotate and structurally identify small molecules based on mass spectrometric data.Objective: The main objective of the CASMI contest was an unbiased evaluation of current methods for annotation and structure elucidation of small molecules. Methods: Participants were asked to define the structures of unknown small molecules based on a set of high resolution MS and MS/MS data provided by the organizers. There were two categories to compete in: best molecular formula (category 1) and best molecular structure (category 2). A total of 42 known and 6 unknown compounds were presented as challenges. Each contestant applied their own approach to solving the challenges. Results: Seven teams from Europe, North America and Japan participated in the contest. In category 1 three teams correctly solved 34/42 molecular formulas. In category 2 the best performing team correctly solved 24/42 structures. No correct solution in category 2 was received for unknown compounds. Conclusion: As long as correct molecular species can be determined, determination of molecular formula from accurate mass data is reliable and robustly performed by the majority of teams. On the other hand, structure elucidation from mass spectrometric data is still a challenging task, particularly for true unknowns.