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In Portuguese, it is common to say that a patient is "undergoing an investigation" of their disease (meaning: the physician is trying to diagnose what they have, i.e., is "investigating" their condition).

This, however, seems wrong in English, I think "investigation" has a sort of legal connotation usually. I'm also unsure whether it's grammatical to say "patient X is undergoing an investigation of / investigating their disease".

From what I gather, "clinical investigation" tends to mean the same as "clinical trials", a research trying to find new treatments or discover new diseases. This isn't the meaning I'm looking for; rather than a case study of sorts, I'd like to refer only to the struggle of a patient and their doctor in finding out which disease they have.

What is an idiomatic and formal way to say that my patient X is "trying to find out" what disease they have?

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I think you have the wrong information.
In idiomatic English a "clinical investigation" is the doctors trying to diagnose what is wrong with the patient. If there is no ambiguity then, like Portuguese, just "investigation" means the same thing. It's OK to say

Patient X is undergoing an investigation of their disease.
or
Patient X is undergoing a clinical investigation.

A "clinical trial" is usually verifying that the new treatment is safe for general use.

The covid vaccine underwent accelerated clinical trials before being rolled out for a mass vaccination program.

All of the above are acceptable, formal ways. Informally you might say

The doctors are trying to find out what's wrong with me.

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