I am a bit hesitant, because I've heard a lot of criticism of the "chemicals turned my frog gay" study by David Skelly mentioned in articles introducing the idea. And of course how the MRA's have glammed onto the whole 'soy boy' phenomena.
It seems to just be a hypothesis for now. But this is what i've found on it:
Another working hypothesis involves the role of endocrine disruptors in transgender etiology. In a letter to the editor, Bejerot, et al. suggested a hypothetical link between endocrine disrupting chemicals and transgenders . They hypothesized a role for endocrine disruptors, especially phthalates. Phthalates are present in some plastics, and there has been an increased concentration in the environment in recent years. Bejerot, et al. suggested that endocrine disruptors may be the cause of high fetal testosterone exposure leading to increased risk of ASD as well as GD . More systematic investigations are required that may also elaborate mechanisms involved in brain development and sexual differentiation.
Research in rats has shown that endocrine disruptors like polychlorinated biphenyls (PCB) profoundly impair the sexual differentiation of female hypothalamus . Also, there is a growing concern that the use of fragrance-containing daily lifestyle materials run parallel with the unprecedented rates of malignancies, neural ailments, teratogenicity, and transgender instances . PCB exposure can lead to altered neuronal activity in hippocampus and identify it as potential environmental risk factors for neurodevelopmental disorders. The mechanism involves probable defects in neuronal Ca++ signaling, increased ryanodine receptor activity and dendritic growth in hippocampal neurons caused by PCP .