Neurons in the third-order auditory nuclei in the brainstem of chicks (nuclei laminares, NL) receive functional innervation from the ipsilateral and contralateral second-order nuclei (nuclei magnocellulares, NM) which is restricted to the dorsal and ventral dendrites respectively. This pattern of innervation in NL is established by embryonic stage 40 (day 15 of incubation). We have examined the distribution of this innervation in both NL at this age or older in embryos from which one otocyst had been removed or damaged on day 3 of incubation. The distribution of functional synapses was determined by analysis of the changes in polarity of field potentials evoked by electrical stimulation of either the ipsilateral or contralateral NM. The distribution of field potential polarity in NL of 40% of recordings in operated embryos and in all sham-operated embryos was the same as that observed in unoperated embryos. However, in the remaining operated embryos, the time course of the field potentials and the changes in the polarity of the responses as the recording electrode penetrated NL were abnormal. The abnormal complexity of responses and the abnormal distribution of field potential amplitude in NL in the operated embryos suggests that loss or damage to the first-order auditory innervation can result in (a) the formation of novel, functional synapses between second-order auditory neurons, and/or (b) disruption of processes that produce segregated innervation of the dendrites of the third-order auditory neurons.