An automated cell injection system and method are described, which can perform automatic, reliable, and high-throughput cell injection of foreign genetic materials, proteins, and other compounds. The system and method overcome the problems inherent in traditional manual injection that is characterized by poor reproducibility, human fatigue, and low throughput. The present invention is particularly suited for zebrafish embryo injection but can be readily extended to other biological injection applications such as mouse embryo, drosophila embryo, and C. elegans injections, capable of facilitating high-throughput genetic research at both academic and industry levels. A novel vacuum based cell-holding device is also provided.