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A functional relationship between brainstem and cortical auditory processing was shown to be abnormal in children with language-based learning problems (LP). Auditory evoked potentials were used to investigate brainstem and cortical responses to the speech sound /da/. The duration of the wave V–Vn complex of the auditory brainstem response was studied, as was the effect of noise on correlations between cortical responses to repeated stimuli. The group of LP children (n = 11) demonstrated abnormal encoding of speech sounds on both individual measures of brainstem and cortical processing; prolonged wave V–Vn duration and pronounced susceptibility of cortical correlations to degradation by noise were both interpreted as reflecting diminished synchrony of response generator mechanisms. Furthermore, the LP group as a whole failed to demonstrate a relationship between brainstem and cortical measures that was demonstrated to be quite strong across all normal children (NL, n = 9). However, a subset of roughly three-quarters of the LP children appeared to demonstrate the normal relationship between brainstem and cortical processing, suggesting that they share a common functional connection with NL children. This relatively normal relationship between brainstem and cortical auditory processing in most LP children, as well as the exceptions to this relationship reflected by a smaller portion of LP children, may delineate different subclasses of auditory-language-based learning problems. This suggests the potential for use of these measures as diagnostic tools.