Motor threshold (MT), as determined by transcranial magnetic stimulation (TMS), is used as a parameter of cortex excitability. In TMS with single or repetitive pulses, stimulus intensities in general are referred to the individual MT, although it is unclear whether MT also reflects the excitability of nonmotor cortical areas such as the visual cortex. Visual cortex excitability can be assessed by thresholds for eliciting phosphenes (phosphene threshold, PT) following TMS over the occipital cortex. The question of a different efficacy of TMS pulses in distinct cortical areas was approached by comparing motor and phosphene thresholds using single-pulse TMS applied to the primary motor and visual cortex. The aim of the study was to clarify, whether NIT and PT correlate with each other and whether NIT possibly serves as a reasonable measure for the excitability of the visual cortex. In 32 healthy volunteers, TMS with biphasic single pulses was applied over the motor and visual cortex with a figure of eight-shaped coil connected to a Dantec MagPro stimulator. NIT and PT were individually measured (percent of maximal stimulator output). Mean PT (61.4 +/- 11.7%) was significantly higher than mean MT (39.4 +/- 5.9%) (p = 0.01). MT and PT did not correlate significantly (r = 0.29, p>0.1). These findings suggest that the NIT does not reflect the excitability of the visual cortex. Regarding excitatory effects, the efficacy of TMS may be different over the motor and visual cortex, likely related to a different excitability of these cortical areas. This should be considered in planning and execution of TMS studies of nonmotor cortical areas. (C) 2003 Elsevier B.V. All rights reserved.