This book constitutes three challenges that were held in conjunction with the 24th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2021, which was planned to take place in Strasbourg, France but changed to an online event due to the COVID-19 pandemic. The peer-reviewed 18 long and 9 short papers included in this volume stem from the following three biomedical image analysis challenges: • Mitosis Domain Generalization Challenge (MIDOG 2021), • Medical Out-of-Distribution Analysis Challenge (MOOD 2021), and • Learn2Reg (L2R 2021). The challenges share the need for developing and fairly evaluating algorithms that increase accuracy, reproducibility and efficiency of automated image analysis in clinically relevant applications.