In many individuals with pattern strabismus, the vertical misalignment varies with horizontal eye position. It has been proposed that these cross-axis effects result from abnormal cross-talk between brainstem structures that would normally encode horizontal and vertical eye position and velocity. The nucleus prepositus hypoglossi (NPH) is an ideal structure to test this overarching hypothesis. Neurons in the NPH are believed to mathematically integrate eye velocity signals to generate a tonic signal related to horizontal eye position. We hypothesized that, in monkeys with A-pattern exotropia and vertical inconcomitance, these neurons would show an abnormally large sensitivity to vertical eye position. Three rhesus monkeys (1 normal and 2 with A-pattern exotropia) were trained to maintain fixation on a visual target as it stepped to various locations on a tangent screen. Extracellular neural activity was recorded from neurons in the NPH. Each neuron's sensitivity to horizontal and vertical eye position was estimated using multiple linear regression and preferred directions computed for each eye. Unexpectedly, the mean preferred directions for the left eye were normal in the monkeys with A-pattern exotropia. For the right eye, there was a clear upward deviation for the right NPH and a downward deviation for the left NPH. In addition, the R2 values were significantly lower for model fits for neurons recorded from the exotropic monkeys. We suggest that vertical inconcomitance results from inappropriate vertical-to-horizontal cross-talk that affects the two eyes differently.