We propose and demonstrate a simple, low-cost, three-dimensional (3D) shape acquisition method for transparent 3D printed microscopic objects. Our method uses ultraviolet (UV) illumination to obtain high-contrast silhouette images of transparent 3D printed polymer objects. Multiple silhouette images taken from different viewpoints make it possible to reconstruct the 3D shape of this transparent object. A 3D shape acquisition system consisting of a UV light-emitting diode, charge-coupled device camera and a rotation stage was constructed and used to successfully reconstruct the 3D shape of a transparent bunny model produced using micro-stereolithography. In addition, 3D printed pillar array models, with different diameters on the order of several hundred micrometers, were reconstructed. This method will be a promising tool for the 3D shape reconstruction of transparent 3D objects on both the micro- and macro-scale by changing the imaging lens.