Fragile X syndrome is the most common inherited form of mental retardation and developmental disorders. It results from a dynamic mutation in the FMR1 gene on the X chromosome, characterized by the expansion of a CGG repeat sequence in the 5'-untranslated region of the gene. Based on the number of CGG repeats, four allele classes are distinguished: normal (5-44 CGG), intermediate (45-54 CGG), premutation (55-200 CGG), and full mutation (>200 CGG). The syndrome is also characterized by mosaicism, the presence of different alleles in different subpopulations of cells. The aim of this study was to compare the results obtained using GeneMapper and AmplideX Reporter software and to determine whether the automated AmplideX Reporter can replace GeneMapper software in routine diagnostics. A total of 130 samples were analysed, including 129 patient samples and 1 negative control sample. The analysed samples covered all four categories of alleles, and mosaicism was detected in 3 samples. Differences in the number of repeats by 1 or 2 CGG triplets between the two programs were found in 41 samples but with no significance in clinical interpretation. In the AmplideX Reporter software, allele splitting was observed in 19 samples, and additional peaks were detected in 11 samples. The comparison showed greater sensitivity and specificity of the AmplideX Reporter software in mosaicism detection due to its automatic calculation of the number of CGG repeats based on the CGG profile and ROX size ladder, as well as its consideration of quality control during the analysis. System optimization is needed to fully satisfy the quality control requirements for each analysed sample and to ensure the accuracy of the obtained results.