Find a medmal lawyer and sue the doctor for medical negligence, assault, and performing an unnecessary procedure without obtaining your consent. If the doctor didn't see the kidney stone, the doctor should have not gone through with the procedure.
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Medical malpractice cases are very expensive and time consuming to prosecute. I agree with Mr. Lassen that the damages you describe are insufficient to interest most lawyers in pursuing your claim.
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An x-ray isn't sufficiently sensitive to "see" a kidney stone. Sometimes it can see it, sometimes not. As they had detected it before, likely on CT or a pyelogram, then it was appropriate for the urologist to continue with the procedure. Taking a biopsy is fairly routine and nothing to be necessarily concerned about. To know more about what was done, you are free to request your medical records or more specifically just the operative report from the procedure.