The bilateral deficit refers to the phenomenon in which homologous muscles produce per muscle less force when contracting simultaneously than when contracting individually. The mechanism underlying the bilateral deficit is still unknown, but the most likely cause is a decline in the activation of motor units during bilateral contractions. In the present study, we used functional magnetic resonance imaging (fMRI) to measure the degree of brain activity during unilateral and bilateral maximal contractions in combination with force and EMG measurements. Subjects performed, in a semi-randomized order, maximal isometric contractions (MVC) with the right index finger, the left index finger and with both fingers simultaneously. During the task, brain activation was measured with a 3 T MR scanner, in combination with force and EMG recordings. The most important activated areas in the brain during the contractions were the sensorimotor cortex (precentral and postcentral gyrus), cerebellum, premotor cortex and supplementary motor area. During bilateral contractions, a significant decline in force and EMG values was found and detailed analysis of the brain activation data showed that this decline was accompanied with a significant decline in the activation of the precentral gyrus. This result suggests that the bilateral decline is the resultant of a decline in input to the primary motor area and shows that the main source of the bilateral deficit lies upstream of the primary motor cortex.