We characterized the visual pathways involved in the stereoscopic recognition of the random dot stereogram based on the binocular disparity employing a functional magnetic resonance imaging (fMRI). The V2, V3, V4, V5, intraparietal sulcus (IPS) and the superior temporal sulcus (STS) were significantly activated during the binocular stereopsis, but the inferotemporal gyrus (ITG) was not activated. Thus a human M pathway may be part of a network involved in the stereoscopic processing based on the binocular disparity. It is intriguing that areas 44 (Broca's area) and 45 in the left hemisphere were also active during the binocular stereopsis. However, it was reported that these regions were inactive during the monocular stereopsis. To separate the specific responses directly caused by the stereoscopic recognition process from the nonspecific ones caused by the memory load or the intention, we designed a novel frequency labeled tasks (FLT) sequence. The functional MRI using the FLT indicated that the activation of areas 44 and 45 is correlated with the stereoscopic recognition based on the binocular disparity but not with the intention artifacts, suggesting that areas 44 and 45 play an essential role in the binocular disparity.