Three-dimensional (3-D) positioning and orientation of embryos/oocytes is necessary to facilitate micromanipulation tasks such as cell injection and cellular structural biopsy commonly performed under a microscope. Conventional cell orientation is performed manually by using a vacuum equipped micropipette to aspirate and release the cell, which is a trial-and-error approach. The conventional method relies heavily on the skill of the operator; it also suffers from low precision, low success rate and low controllability. These drawbacks illustrate the need for a systematic 3-D cell rotational system to automate the cell orientation process. In this paper, we present a noninvasive single cell rotation system that can automatically orientate a zebrafish embryo to a desired position when both the cytoplasm and the yolk are in the focal plane. A three-point-contact model for cell rotation that involves a custom-designed rotational stage is introduced to provide precise rotational position control. A vision recognition algorithm is also proposed to enable the visual servoing function of the system. Experimental results show that the proposed system can achieve high success rates of 92.5% (x-axis rotation with 40 trails) and 97.5% (about the z-axis with 80 trails). The system can also successfully complete 3-D cell orientation at an average speed of 31 s/cell with a high in-plane rotation accuracy of 0.3 (°) . As a high precise, high controllable and deterministic cell manipulating system, it provides a starting point for automated cell manipulation for intracytoplasmic sperm injection and embryo biopsy for preimplantation genetic diagnosis.