Microcrystals of zinc citrate dihydrate (ZnCit), a nucleating agent of poly(L-lactic acid) (PLLA), were magnetically oriented to obtain a three-dimensional magnetically oriented microcrystal array (3D-MOMA). The structure determined by X-ray analysis of the 3D-MOMA agreed well with that determined using a single crystal. The relationship between the magnetic and crystallographic axes was determined. Since the ZnCit crystal reportedly induces epitaxial growth of PLLAs, their three-dimensional alignment is expected to induce three-dimensional alignment of the PLLA crystals.