Early-onset gender identity disorder (EO-GID) describes a strong and persistent development of cross-gender identification. Using structural magnetic resonance imaging (sMRI) and blood samples, we studied 13 female to male patients with EO-GID and compared them to 11 biological female controls. We found that the EO-GID group in comparison to its control group showed several significant differences in regional brain volumes. These include an increase in cerebral gray matter and a decrease in volume of cerebellar white matter in the mid anterior and posterior part of the corpus callosum. Furthermore, we showed statistically significant relationships between hormone levels and regional brain volume. These include relationships between the free thyroid hormone thyroxine (T4) and volumes of the frontal lobe, the temporal lobe and cerebral white matter; between sex-hormone binding globulin (SHGB) and the frontal lobe; as well as between thyroid-stimulating hormone (TSH) and cerebral gray matter. The results of regression analyses indicate that brain volume (outcome variables) decreases with the lower thyroid hormone levels (predictor variables). We propose that abnormal hormonal development of thyroid hormones influences white matter volume in our EO-GID group. Such an abnormal development further might affect both structural and functional properties of the brain.