The medical understanding of autism has changed since it was first defined by Kanner. Nowadays medicine identifies many medical abnormalities and diseases, which may underline or aggravate the cognitive aspect, behavioural issues and general health in autists. This includes chronic inflammation of gastrointestinal tract, dysbiosis, maldigestion, malabsorption, malnutrition, food intolerance, allergies, chronic viral, fungal and bacterial infections, impaired kidney function, impaired detoxification of endo- and exotoxins, disorders of metal ion transportation. Treatment of the above mentioned conditions combined with improving detoxification mechanisms, followed by a special diet and individually customized supplementation of nutritional deficiencies may lead to the improvement of the functioning of these patients, changing their level of functioning and self-dependence. The aim of this paper is to present medical problems of children with autism which may be identified and treated by general practitioners as a review of current medical papers related to Autism Spectrum Disorder, in the context of author's professional experience, based on the medical cases from author's practice.