This is a unique case of intrachromosomal triplication of the X chromosome q arm detected with cytogenetic and spectral karyotyping in a 21-year-old woman with primary amenorrhea, who had been referred because of primary hypergonadotropic hypogonadism and Mullerian hypoplasia. Intrachromosomal triplications are rare rearrangements resulting in partial tetrasomy. Since 1993, at least 34 cases of intrachromosomal triplications involving 9 different chromosomes have been reported. The vast majority of the reported triplications are on the 15th chromosome, arised de novo and had middle inverted repetitions. In this report the genotype-fenotype correlation in a case of primary amenorrhea associated with triplication of the X chromosome q arm and the possible mechanisms of this rearrangement are discussed. Further the clinical usability of SKY analysis as a molecular cytogenetic tool in searching for genomic instability arising from cytogenetic rearrangements is highlighted.