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There's a world of difference between "Which of these two options defines your gender identity and sex organs?" and "Which grammatical gender form should we use for words when we talk about you?". The former is a deeply personal question with unclear benefit; the latter is a specific question about how you want the site to do a specific thing it needs to do. (Does it really need to do that? Why exactly are you asking about gender?)

I have an anecdote that I think fits your assumption. It comes from my years in the Danish public sector where some of the systems are many decades old. In Denmark we’re all issued a social security number that is designed in such a way that the last number of it, is odd for males and even for females.

To make things short and somewhat anonymous, we had several systems that couldn’t handle people changing the “gender” of their social security number. They could handle you getting a new social security number, but it had to be of the same “gender” as your previous.

This makes no real sense, as it’s just a number and all these systems handle both types of numbers. But there we were, and it took us several years to get to a point where we could accommodate an employee changing the “gender” of their social security number.

So sometimes, developers do weird things because of their assumptions.

Ps. I’ve put “gender” in “”s because I’m unsure what the right word is in English.

It could help an e-commerce site predict what kind of clothes to recommend, or otherwise segment you for marketing

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