Background Mobius sequence is a rare condition usually defined as uni- or bilateral congenital facial weakness with impairment of ocular abduction. Mental retardation is estimated to occur in 10-15% of cases, but at present there have been no studies focusing on the intellectual capacities of children and adolescents with Mobius sequence. Methods Twenty-three children and adolescents aged 6-16 years could be recruited following a request of the German Mobius foundation. The primary caregivers of all subjects filled out a special questionnaire to compile personal, somatic and psychosocial history of the probands. All subjects had a physical examination. To assess intellectual capacities, the German version of the Wechsler Intelligence Test-III (WISC-III) was administered. In case of a severe mental retardation, the Vineland Adaptive Behavior Rating Form was used as an alternative. Results Twenty-two subjects [12 males, 10 females; mean age: 11.3 (6-16) years] could be included; 21 could be examined with the WISC-III. Compared with the normative sample, Full Scale IQ (mean: 92.05; standard deviation: 14.84) was significantly lower (P = 0.023) which was the consequence of a very low Performance IQ (mean: 80.48; standard deviation: 15.84). Compared with the normative sample, the results of all performance subtests were significantly lower (P = 0.033-0.000), whereas verbal subtest scores did not differ or were even higher ['Similarities' (P = 0.026) and 'Vocabulary' (P = 0.019)]. Verbal IQ (mean: 106.24; standard deviation: 15.31) was not significantly different from the normative sample. Two boys met ICD-10 criteria for mental retardation. Full Scale IQ was not predictive for academic success. Conclusions The WISC-III is not an adequate predictor for academic success in Mobius patients; intelligence tests which are less dependant on time constraints should be preferred for subjects with Mobius sequence.