The genitals or sexual organs were the reproductive organs in most humanoid species. In the Human species, the males and females had different sexual organs. (TNG: "The Outcast")
The fact that different humanoid species can interbreed implies that most humanoids had distinct male and female sexual organs. A notable exception were the J'naii.
In at least one species, the genitals were located in the right knee. This was different from many other species. This did not, however, affect the sensitivity of the organ. (Star Trek VI: The Undiscovered Country)
When Chief Miles O'Brien made an unsuccessful attempt to retrieve his time lost daughter Molly from Golana, he said "Bollocks," which was a colorful metaphor used to describe the testicles. (DS9: "Time's Orphan")
Jadzia Dax had her ovaries operated on in an attempt to be able to conceive with Worf. (DS9: "Tears of the Prophets")
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