As part of multidisciplinary surveys of three Behavioural Phenotype Conditions (BPCs); Möbius sequence (Möbius), CHARGE syndrome (CHARGE) and oculo-auriculo-vertebral spectrum (OAV), autism spectrum conditions (ASCs) was diagnosed in 45%, 68% and 42% of the individuals, respectively. Diagnostic difficulties due to additional dysfunctions such as mental retardation (MR), impaired vision, reduced hearing and cranial nerve dysfunction, were experienced in all three BPC groups. The applicability of current autism diagnostic instruments, such as the Autism Diagnostic Interview-Revised (ADI-R), the Childhood Autism Rating Scale (CARS) and the Autistic Behaviour Checklist (ABC), in individuals with ASCs and Möbius/CHARGE/OAV was analysed. Use of an extensive battery of diagnostic instruments, including both observational schedules and parent interviews, and, if possible, independent judgements from two clinicians, is essential in the diagnostics of ASCs in these individuals. Further, in individuals who are deaf and blind the applicability of current autism diagnostic instruments is highly questionable.