Studies have shown that individuals with language disorders, such as developmental dyslexia and specific language impairment, exhibit impairments in the processing of brief, successive, or rapidly changing auditory information. It is also the case that a higher rate of autoimmune disorders have been identified in those with language-based learning disorders and, conversely, that individuals with autoimmune disorders show a higher incidence of language-related disorders. The rapid auditory processing (RAP) deficits described for older individuals with language impairments may also be used as a behavioral marker to identify infants at higher risk for language delays. Thus, we were interested in examining RAP abilities in a subset of infants with a positive family history of autoimmune disorders. Eleven infants from our ongoing prospective longitudinal studies were identified based on parental response to a question about the presence of a family history of autoimmune disease and compared to 11 matched controls. The RAP threshold of each infant was assessed at 6 and 9 months of age using a conditioned head-turn procedure (using tone pairs with brief interstimulus intervals) and an auditory-visual habituation-recognition memory task using computer-generated consonant-vowel syllables (/ba/ vs. /da/). A visual habituation-recognition memory task that did not require processing of brief temporal cues was also administered. Group differences emerged on the infant RAP tasks, and on language outcome measures at 12 and 16 months of age. Infants from families with a history of autoimmune disorder had significantly higher (i.e., poorer) RAP thresholds and lower language scores than did control infants, whereas visual discrimination scores did not differ between family history infants and controls. Moreover, when brief auditory cues were necessary for the discrimination of /ba/ vs. /da/, infants with a family history of autoimmune disorder performed significantly more poorly than did controls. These findings lend support to the hypothesis that a similar mechanism, perhaps a neural-immune interaction, may underlie the observed co-occurrence of autoimmune disorders and learning impairments.