The 28-year-old man, identified only as Mr L, was born and registered as female, but since 1998 has undergone hormone treatment and breast removal.
His doctors say they will complete the operation only when legal conditions are established.
The case at the European Court of Human Rights claims his rights were violated.
His lawyers said his rights had been breached on several grounds, including respect for private life, the right to marry, discrimination and the prohibition of degrading treatment.
Mr L has adopted a Slavic name to conceal his gender - Lithuanian names are gender-specific.
But he says he suffers a vast amount of daily embarrassment because the prefix on his official documents identifies him as a woman.
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