Advancing the state-of-the-art in large-scale biomedical semantic indexing and question answering is the main focus of the BioASQ challenge. BioASQ organizes respective tasks where different teams develop systems that are evaluated on the same benchmark datasets that represent the real information needs of experts in the biomedical domain. This paper presents an overview of the ninth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2021. In this year, a new question answering task, named Synergy, is introduced to support researchers studying the COVID-19 disease and measure the ability of the participating teams to discern information while the problem is still developing. In total, 42 teams with more than 170 systems were registered to participate in the four tasks of the challenge. The evaluation results, similarly to previous years, show a performance gain against the baselines which indicates the continuous improvement of the state-of-the-art in this field.