Animal phobias in young people with autism spectrum disorders (ASD) and intellectual disability (ID) can provoke behaviours that put them at risk and impede access to the community. Previous studies suggest that cognitive behavioural therapy including systematic desensitization and modelling are effective for people with ID, including those with comorbid ASD. Methods of adapting such treatment to people with little spoken language are not well described, and ethical issues concerning both young people and animals during treatment have not been addressed. The aim of this study was to describe, using a case series of consecutive referrals: (1) adaptations to systematic desensitization when communication of the young person is impaired, and (2) the ethics of involving animals in therapeutic interventions. Treatment was planned based on the use of systematic desensitization with a hierarchy of feared situations using visual symbols and schedules to communicate with the participants. Five young people with ASD, severe ID and minimal language were successfully treated for dog phobia. Modifications to treatment included both the use of non-verbal means of communication including printed symbols and graded activities such as jigsaw puzzles and picture matching to present information to clients in a more finely graded format. The treatment of specific phobias is possible with the use of minimal language provided that a variety of individualized stimuli approximating to the feared objects are developed and the safety of all participants is respected. Further work is required to develop sufficiently flexible treatment protocols, which in turn would enable a randomized controlled trial.