Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder marked by difficulties in communication, social interaction, and restricted, repetitive behaviors. The gut microbiota has emerged as a key factor in the gut-brain axis relevant to ASD. We conducted a cross-sectional study comparing the gut bacterial composition of children with ASD (n=29) and their neurotypical siblings (NT, n=29). To minimize environmental and lifestyle confounders, all pairs were 4 to 10 years old and cohabiting in the same household in Uruguay. We used full-length 16S rRNA gene (V1–V9) sequencing with the latest R10.4.1 Oxford Nanopore Technologies chemistry, enabling high-resolution microbial characterization. We found that the ASD group was enriched in taxa like Sellimonas, while the NT group showed enrichment of genera like Faecalibacterium and Coprococcus. Furthermore, we found GI symptoms to be significantly more prevalent in the ASD group and some bacterial genera associated with GI symptomatology. In addition, we explored the association of pharmacological treatments. Antipsychotic use was associated with reduced Akkermansia abundance, whereas melatonin and methylphenidate use were associated with the enrichment of Negativibacillus. This study provides novel insights into the gut microbiome of Uruguayan children with ASD, delineating the influence of GI symptoms and pharmacological load on microbial diversity and composition.