There has been little or no evidence of brainstem auditory evoked potentials (BAEPs) among infants with iron deficiency (ID) that is not severe enough to cause anemia. To our knowledge, the effect of ID on auditory functions and/or potentials has not been investigated previously, though it seems reasonable that it should be associated with BAEP measures intermediate between those observed in iron deficiency anemia (IDA) and in iron sufficiency, considering the role of iron in myelin formation and maintenance. We therefore aimed in this study to investigate the effect of ID on BAEPs by comparing three groups of infants with ID, IDA and iron sufficiency (control) both before and after iron treatment (in iron-deficient groups). Three groups of infants (IDA, n = 25; ID, n = 24; Control, n = 44) were compared on the basis of hematological laboratory parameters and BAEP measurements both at entry into and after (12 weeks treatment with oral iron in IDA and ID groups) the study. BAEP measurements recorded at 85 dB both at entry into and after the study were not significantly different among the groups, although a sufficient response to iron treatment was achieved in iron-deficient groups (Group I and Group II). The only positive finding determined in our study was a slight decrease in latencies obtained at the end of the study when compared to the pre-study values in all three groups of the study in accordance with the expected age-dependent developmental changes. Although no negative electrophysiological effect of ID on brainstem auditory functions was found in the present study, further longer term (late childhood or adult) studies are necessary to elucidate the relationships among anemia (maybe other than IDA), ID and auditory functions, and clinical implications of hearing loss (if any) should be questioned.