We propose a novel on-chip 3D cell rotation method based on a vibration-induced flow. When circular vibration is applied to a microchip with micropillar patterns, a highly localized whirling flow is induced around the micropillars. The direction and velocity of this flow can be controlled by changing the direction and amplitude of the applied vibration. Furthermore, this flow can be induced on an open chip structure. In this study, we adopted a microchip with three micropillars arranged in a triangular configuration and an xyz piezoelectric actuator to apply the circular vibration. At the centre of the micropillars, the interference of the vibration-induced flows originating from the individual micropillars induces rotational flow. Consequently, a biological cell placed at this centre rotates under the influence of the flow. Under three-plane circular vibrations in the xy, xz or yz plane, the cell can rotate in both the focal and vertical planes of the microscope. Applying this 3D cell rotation method, we measured the rotational speeds of mouse oocytes in the focal and vertical planes as 63.7 ± 4.0° s−1 and 3.5 ± 2.1° s−1, respectively. Furthermore, we demonstrated the transportation and rotation of the mouse oocytes and re-positioned their nuclei into a position observable by microscope. Three-dimensional cell observation and manipulation, required during cellular surgery, rely on proper orientation of the target cell. Conventional cell rotation techniques using microscopic hand-like devices demand sophisticated equipment and highly skilled operators. Additionally, existing on-chip approaches exploiting electric, magnetic and optical forces involve intricate structures that are complex to fabricate. To simplify these systems, Takeshi Hayakawa and co-workers from Nagoya University, Japan, have developed a microfluidic chip that controls cell rotation through vibration. The chip consists of a glass surface decorated with three small pillars in a triangular arrangement. To achieve stable motion, the researchers apply in-plane and vertical circular vibrations, creating local vortexes around the pillars that cause a cell placed at their centre to rotate. This simple, high-performance method is expected to play a central role in future biotechnology research.