Background: Facioscapulohumeral muscular dystrophy (FSHD) occurs as a consequence of genetic deletion of D4Z4 repeats on chromosome 4q35. Onset of FSHD is earlier in males, suggesting that testosterone may trigger the disease. In accordance, the rapid progression of disease in women after menopause suggests a protective role for estrogen and progesterone. No studies have examined levels of all these hormones in relation with the severity of FSHD. Aims: To evaluate the possible correlation between the severity of FSHD with sex hormones, age, and genetic deletion on chromosome 4q35. Subjects and Methods: D4Z4 repeat units were investigated in 33 patients (19 males/14 females) with FSHD. In the blood samples, luteinizing hormone, follicle-stimulating hormone, free estriol, estradiol, free testosterone and total testosterone, progesterone, 17-OH progesterone, prolactin, albumin, and fibrinogen were measured. The severity of FSHD was identified using a Clinical Severity Score (CSS) scaling system. Spearman’s correlation and regression analyses were performed as statistical analyses. Results: Age (P = 0.001, r = 0.541) and total testosterone (P = 0.045, r = 0.351) were positively correlated, and the progesterone/total testosterone (P = 0.025, r = −0.390) and estradiol/total testosterone ratios (P = 0.025, r = −0.389) were negatively correlated with the severity of FSHD. Conclusions: Our results indicate that age, total testosterone, ratios of estradiol and progesterone to total testosterone, but not deletion on chromosome 4q35, have a significant relation with the severity of FSHD. Given that both estrogen and testosterone treatment are considered in therapy, our results suggest that estrogen and progesterone but not testosterone are likely to be more effective on the severity of FSHD.