Turner syndrome (TS) is the most common cause of short stature and delayed puberty in females. Approximately half of the patients have the classic form with a genotype of 45,XO, one-fourth of patients have different mosaic forms, and the remaining one-fourth have structural abnormalities on the X chromosome. Among the structural abnormalities, the most common is isochromosome Xq. Females with structural variants of TS can present with delayed menarche, amenorrhea, and infertility rather than classic manifestations of TS. This study describes two rare variants of TS. One was a structural abnormality on the X chromosome, 46X,iso(Xq), and the other involves a mosaic variety of TS, including isochromosome X in the form of 45,XO/46X,iso(Xq). Both patients presented with short stature and secondary amenorrhea without classic manifestations of TS. In TS with or without mosaicism, the frequency of isochromosomes is reported to be about 15% to 18%. Owing to the absence of classical manifestations of TS, diagnosis may be delayed or missed. Therefore, females of short stature with secondary amenorrhea should be evaluated for rare variants of TS by chromosomal analysis.