We report two patients with deafferentation pain secondary to central nervous system lesions who were evaluated by noninvasive magnetic coil stimulation of the motor cortex followed by electrical motor cortex stimulation with epidural electrode array implantation. Magnetic coil stimulation was very useful to estimate the effect of electrical stimulation. Our first patient was a 52-year-old man who experienced a left putamenal hemorrhage at the age of 48. Two years later, he had paresthesias and intractable pain in the extremities and face on the right side. Pain was resistant to barbiturates but responded to magnetic coil stimulation of the motor cortex. Electrical motor cortex stimulation provided excellent relief from the pain. The second patient was a 43-year-old man who was suffering from congenital cerebral palsy for which left thalamotomy was performed two times, at the ages of 9 and 13. He began to experience intractable pain on the right side 20 years later. Although barbiturate administration was effective for pain relief, neither magnetic coil stimulation nor electrical stimulation of the motor cortex gave relief from pain.