Children with autism spectrum disorders (ASD) are characterized by repetitive behavior and difficulties in social communication. In addition, comorbidity with intellectual disability represents an added difficulty for social communication and the expression of emotions and physical discomfort. Identifying pain is a relevant factor to implement adequate medical and educational treatment. Similarly, gastrointestinal symptoms (GS) and autism symptoms related to sensitivity to certain foods, textures, etc., are associated factors. Thus, there is a high comorbidity of GS in children with ASD. However, standardized instruments are required to assess pain, sensitivity, and GS in the autistic population. In this sense, the so-called Microbiota-intestine-brain axis suggests that there is a dysbiosis or alteration of the gut-microbiota (GM) in ASD, which can trigger the appearance and development of all these symptoms in the child. Recently, a meta-analysis has found low levels of the bifidobacterium bacteria in children with ASD. This bacterium is involved in the regulation of neurotransmitters such as dopamine, etc., that regulate the emotional state. The abundance levels of that bacteria are usually higher in the first two years of the child’s life. For this reason, this decrease in bifidobaterirum provides information on neurodevelopment and the functioning of the Microbiota-intestine-brain axis in ASD. In recent years, there has been an increase in the industrial development of probiotics to treat the symptoms of different mental disorders. However, there are a small number of studies that analyze the efficacy of probiotics in ASD, most of the compounds being based on the bacteria lactobacillus. Future research should consider the efficacy of bifidobacterium-based probiotic compounds. A clinical trial is required to analyze pain symptoms, GS, repetitive behaviors, anxiety levels between the experimental group and a control group, using placebos and different types of probiotics.