BACKGROUND: Nearly all females with Turner syndrome (TS) suffer from gonadal dysfunction causing hypergonadotropic hypogonadism and estrogen deficiency. Estrogen has a wide range of beneficial effects throughout the female body, where estrogen receptors are localized in most tissues. Consequently, estrogen deficiency causes cardiovascular, endocrine and physiological changes, impairing TS patients’ health profile. Patients with TS are subject to hormone replacement therapy (HRT) from puberty to menopause, as either oral or transdermal treatment. HRT is a well-implemented treatment; however, evidence concerning the optimal route, dose and monitoring of estrogen therapy is greatly lacking. AIM: We aim to compare the long-term effects of transdermal versus oral estrogen replacement therapy in women with TS. METHODS: A 14-month, randomized, crossover study including 50 females with TS and 50 healthy, age-matched female controls. Patients are randomized to receive 6 months of oral and 6 months of transdermal estrogen therapy. Treatment doses of estrogen are individualized to normalize levels of gonadotropins. Effects on cardiovascular, coagulation, pharmacological, endocrine and physiological endpoints are studied. PERSPECTIVES: The outcomes of this project will be crucial for optimizing estrogen replacement therapy in TS patients. In addition, our results can likely be extended to a wider population of females with premature ovarian failure. Our goal with the present study is to provide basis for new and improved national and international recommendations for HRT in TS patients.