Board Thread:Questions and Answers/@comment-33790467-20190814010218/@comment-995426-20190821083616

And I don't think any official version of TMNT has ever shown or specified what kind of private anatomy can be found on mutant turtles. We know they have it and that it's fully functional, because of her, and we know the turtles can have biological children, because of her. But we've never actually seen what the anatomy looks like on mutant turtles&mdash;in the entire multiverse, I think we've only seen it on s, because of him.  Of course, maybe it's better we don't see official turtle privates, lest we ruin the head canons of fanfic writers everywhere.

But, for the sake of argument:
 * What if they had cloacae? And what if Splinter was educated in turtle biology and knew what to look for?  Mutant turtles are more or less part human, so even if they did have them, they may not necessarily be in the same position as in non-mutant turtles, making inspection uncertain.
 * What if they had, *ahem,* something shaped like that of a human male? Would be the simplest outcome, as it's very difficult to mistake what it looks like.  This option is plausible if the anatomy is present but out of view just inside the bottom of the shell.  It remains plausible in Rise of the TMNT even if not hidden, because they all wear boxer briefs, which they may actually be wearing for that purpose.
 * It would actually be funny if they were human-shaped, but could not be inspected when they were still young, if tthe anatomy needed to "descend" into place in adolescent development, whether or not it's visible outside the shell.
 * The simplest option is for them to explain their own gender to Splinter when they are able to do so.