The present results using repeated measures of auditory P300 amplitude in the same individuals confirm previous findings using visual P300 amplitude by identifying three trajectory classes during childhood and adolescence. The present findings extend our previous results by showing that trajectories obtained at the earliest ages (8–12) are most likely to be the most robust predictors of familial risk, especially in males, and are additionally related to muscarinic receptor variation. Because low amplitude P300 in childhood predicts substance use outcome by young adulthood, identifying the factors associated with presence of the lower P300 amplitude trajectory in childhood provides important clues regarding possible mechanisms of susceptibility.