Estrogen concentration has been suggested to play a role in tendon abnormalities and injury. In physically active postmenopausal women, hormone replacement therapy (HRT) has been suggested to decrease tendon diameter. We hypothesized that HRT use and physical activity are associated with Achilles tendon size and tissue structure. The study applied cotwin analysis of fourteen 54- to 62-yr-old identical female twin pairs with current discordance for HRT use for an average of 7 yr. Achilles tendon thickness and cross-sectional areas were determined by ultrasonography, and tendon structural organization was analyzed from the images using linear discriminant analysis (LDA). Maximal voluntary and twitch torques from plantar flexor muscles were measured. Serum levels of estradiol, estrone, testosterone, and sex hormone binding globulin were analyzed. Total daily metabolic equivalent score (MET-h/day) was calculated from physical activity questionnaires. Results showed that, in five physically active (MET > 4) pairs, the cotwins receiving HRT had greater estradiol level (P = 0.043) and smaller tendon cross-sectional area than their sisters (63 vs. 71 mm(2), P = 0.043). Among all pairs, Achilles tendon thickness and cross-sectional area did not significantly differ between HRT using and nonusing twin sisters. Intrapair correlation for Achilles tendon thickness was high, despite HRT use discordance (r = 0.84, P < 0.001). LDA distinguished different tendon structure only from two of six examined twin pairs who had a similar level of physical activity. In conclusion, the effect of HRT on Achilles tendon characteristics independent of genetic confounding may be present only in the presence of sufficient physical activity. In physically active twin pairs, the higher level of estrogen seems to be associated with smaller tendon size.