Turner syndrome (TS) with an isochromosome mosaic karyotype 45,X/46,X,i(X) (q10) is an unusual variant, with only an 8-9% prevalence among women with TS based on international studies and 15% of all TS in the Philippines. Clinical features are atypical and any case should be investigated to detect potential complications. A 20-year-old female came in due to amenorrhea and alopecia. Physical examination revealed short stature, cubitus valgus and Tanner Stage 1 pubic hair and breast development. Transrectal ultrasound revealed absent ovaries and infantile uterus. Hormonal evaluation revealed hypergonadotropic hypogonadism. Bone aging was that of a 13-yearold for females with non-fusion of epiphyseal plates. Cytogenetic study revealed 45,X [37]/46, X, i (X) (q10)[13]. This is consistent with a variant Isochromosome Mosaic Turner Syndrome (IMTS). She was screened for medical complications. Audiogram and two-dimensional echocardiography were unremarkable. She has dyslipidemia and was given a statin. She has subclinical hypothyroidism with positive test for anti-thyroglobulin antibody. Her intelligence quotient (IQ) was below average. She received conjugated estrogen and progesterone that patterned the hormonal changes in a normal menstrual cycle. On the third week of hormonal therapy, she developed breast mound and on the fourth week, she had her first menstrual period. Her alopecia spontaneously resolved. The case is a variant of Turner Syndrome requiring supportive, medical and psychological care.