Research and clinical applications, such as microinjection and polar-body biopsy involve 3-D rotation of mammalian oocytes/embryos. In these cell manipulation tasks, the polar body of an embryo/oocyte must be made visible and properly oriented under optical microscopy. Cell rotation in conventional manual operation by skilled professionals is based on trial and error, such as through repeated vacuum aspiration and release. The randomness of this manual procedure, its poor reproducibility, and inconsistency across operators entail a systematic technique for automated, noninvasive, 3-D rotational control of single cells. This paper reports a system that tracks the polar body of mouse embryos in real time and controls multiple motion control devices to conduct automated 3-D rotational control of mouse embryos. Experimental results demonstrated the system’s capability for polar-body orientation with a high success rate of 90%, an accuracy of 1.9, and an average speed of 22.8 s/cell (versus averagely 40 s/cell in manual operation).