The alignment of transmitter coils for the three-dimensional electromagnetic articulograph (3D-EMA), an instrument used to measure articulatory movements, was studied. Receiver coils of the 3D-EMA are used as position markers and are placed in alternating magnetic field produced by multiple transmitter coils. The estimation of the state (the position and orientation) of each receiver coil is based on the minimization of the 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 irrespective of small signal error at a specific portion of the measurement region. The existence of the non-uniqueness problem in the position estimation 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 for any pair of states in the measurement region and evaluated the alignment by performing computer simulations and actual measurement. As a result, a measurement accuracy of approximately 0.4 mm was obtained.