Here we demonstrate the fabrication of non-spherical hydrogel microstructures that are useful as building blocks for tissue engineering, by utilizing non-equilibrium aqueous two-phase systems (ATPS) in microchambers. A dextran (Dex) solution containing cells and hydrogel precursor was introduced into microfabricated chambers, which was gradually shrunk and deformed after pouring a polyethylene glycol (PEG) solution. By further adding a gelation agent, we successfully obtained non-spherical (toroidal or cup-shaped) cell-laden hydrogel microstructures. We were able to control the hydrogel morphology by using microchambers with different geometries, changing the compositions of the solutions, and modifying the surface property of the microchamber.