Several methods of quantifying prepulse inhibition (PPI) of eyeblink responding were compared in adult volunteers. Blink-eliciting stimuli were noise bursts at 85 or 100 dB, and prepulses were also noise bursts, at 55 or 70 dB and lead intervals of 60 or 120 ms. PPI was evaluated by comparing reactivity on prepulse and control trials within participants using the following methods: (1) difference between reactivity on prepulse and control trials; (2) reactivity on prepulse trials divided by that on control trials (proportion of control); (3) difference between reactivity on prepulse and control trials, divided by that on control trials (proportion of the difference from control); (4) range correction (maximum minus minimum reactivity, divided by the range of reactivity), across all control and prepulse trials; (5) z scores across all prepulse and control trials. Prepulses inhibited eyeblink response magnitude in all cases. Proportion of difference was the method least affected by differences in control reactivity, and is the preferred method to use when quantifying PPI, both from a practical and a neurophysiological perspective.