In the auditory system, cortical event-related potential amplitudes are enhanced during selective attention within the auditory channel. In the case of brainstem responses, however, the results are less clear since only a few studies have reported attention effects. Nearly all of these studies have used click stimuli to elicit the brainstem auditory evoked response (BAER). In the present study, pure tones (200 and 400 Hz) elicited the brainstem frequency-following response (FFR) in a task that maximized channel separation by presenting different frequencies to each ear. Twelve male and 12 female subjects participated. Perceptual sensitivity (d') showed an overall right ear advantage (REA) that did not depend on gender or stimulus frequency. FFR averages were enhanced by digital filtering, the 25 ms response was partitioned in half, and quantified by fast-Fourier analysis. Results of the statistical analysis showed a significant Attention x Frequency x Half interaction. Thus, whether or not component amplitudes were larger during attention depended on the particular stimulus and temporal location within the FFR. These results are more complex and time variant than would be predicted by the hypothesis that attention only enhances evoked response amplitudes. Nevertheless, these results suggest that some form of attention-related modulation may be occurring at the level of the brainstem. The present results provide additional support for a peripheral gating mechanism in humans, which has been claimed in a minority of BAER studies. The FFR may provide additional useful information since it presumably depends on phase-locking neural elements, rather than on-units activated by acoustic transients.