The alignment of the transmitter coils for the three-dimensional electromagnetic articulography (3D-EMA), an instrument used to measure articulatory movements, was studied. The receiver coils of the 3D-EMA are used as position markers and are placed in an alternating magnetic field produced by multiple transmitter coils. The estimation of state (the position and orientation) of each receiver coil is based on the minimization of signal error between the measured and predicted receiver signals using a model of the magnetic field. Previous studies report a noticeable increase in the position estimation error at a specific portion of the measurement region irrespective of small signal error values. The existence of non-uniqueness in the position estimation problem is hypothesized to be the cause of this problem. To resolve the problem, we optimized the alignment of the transmitter coils by maximizing the difference between the receiver signals at any two states in the measurement region and evaluated the alignment using a computer simulation and an experiment. As a result, a measurement accuracy of approximately 0.4 mm was obtained.