Fragile X syndrome (FXS) is the most common cause of inherited intellectual disability. The most common etiology of the syndrome is expansion and methylation of a CGG trinucleotide at chromosome region Xq27.3 involving FMR1 (fragile X mental retardation 1 gene). This disorder is commonly underdiagnosed in children and adolescents, given the high clinical variability. In Brazil, molecular diagnosis of FXS by CE does not exist in the public health system. The current standard for separation and identification of DNA fragment sizes is 50 cm CE, which is uncommon in public genotyping laboratories. This study describes the standardization of 36 cm CE for fragment analysis of samples from patients with intellectual disability suggestive of FXS. Genomic dsDNA was isolated from patients and amplified by PCR using the FMR1 AmplideX (R) Kit. It was then possible to detect changes in repeat length of FMR1, such as full mutation and premutation. Thus, the proposed standardization proved to be effective for the diagnosis of FXS, permitting suitable genetic counseling for families. Inclusion of molecular testing such as this in the Brazilian public health service bridges the gap between available technologies and effective diagnosis, universalizing access to genetic testing in central Brazil.