I think it's often a combination of both depending on your symptoms

Doctors diagnose chronic kidney disease based on kidney damage and glomerular filtration rate. What usually happens is that during routine labs and urine tests they see things that aren't normal. For example, people should not have blood or protein in their urine. This is a good sign that there is a problem with the kidney. Second they look at labs such as your serum creatinine, BUN (blood urea nitrogen) and the labs calculation of your estimated GFR (glomerular filtration rate). If any of these numbers are off, then there is a problem. The doctor then discusses with you his concerns. If there is a family history of genetically inherited kidney disease, such as PKD, then he will suggest an ultrasound to determine if that's what you have. If there is no family history of PKD, then he will look at your own health risks for developing chronic kidney disease, IE. are you diabetic, do you have high blood pressure that's uncontrolled, do you have PVD or CVD (peripheral or cardiovascular disease). Sometimes the doctor has to get a biopsy of the kidney to determine what processes are taking place.
So, to answer your question, the National Kidney Foundation's guidelines to determine CKD is based on kidney damage and glomerular filtration rates.
Hope this helps.
Tami

This is tenizie again: Isn't there any other condition that can cause what Tami67 said such that there could be mis-diagnosis if ALL relevant tests are not done? Someone told me that doctors once said he had a kidney mulfunction when all along it was a hernia!?

More often than not, people are mis-diagnosed with PKD, not the other way around. People can develop "simple cysts" on their kidneys for no apparent reason and often general practitioners have mislabled someone as having PKD.
When someone is getting a work up to be a possible kidney donor, those doctors are extremely thorough, after all, that persons life depends on it. If the center he went to for evaluation to donate a kidney says he doesn't have PKD, then you can rest assured that he doesn't.
There is a lot of information available on the web regarding how PKD is diagnosed and most if it is to ensure that people are wrongly diagnosed with PKD. Because this disease is so distinctive and because we know that the kidneys develop cysts by a certain age if you have PKD1 and at a later age if you have PKD2, the gold standard says that if there are no cysts in the kidneys via ultrasound after the age of 30, then you don't have the disease.
Here is a link that talks about diagnosis of PKD: http://www.pkdiet.com/pdf/pkd2.pdf
This link is from a symposium on PKD from 1999, but the criteria has not changed. If anything it has become more stringent.
As to your question in your comment, a general practitioner may misdiagnose a number of things over his lifetime, but a trained nephrologist or specialized transplant clinic will not. That's their job, to ensure that someone does not have a serious illness or disease that would make them inelegible to donate an organ.
I understand your fears and concerns and once again, I would support getting an MRI/MRA to rule out any aneurysm, but people develop aneurysms all the time, without having PKD and no one ever really knows why.
I hope the link helps. Let me know if you have any questions.
Tami

Tenzie,
SO SORRY! I thought I was posting to a different thread!Please disregard my previous post!! (However, I did post some important information on how PKD is diagnosed and a link to a page on diagnosis of PKD that might be helpful).
As to your question, there are several diseases out there that can affect your kidney's besides PKD or diabetes or high blood pressure, although diabetes and high blood pressure are the leading cause of renal failure.
Here are just a few:
Systemic Lupus erythematosus
Glomerularnephritis of any type
Goodpasture Syndrome
Wegeners Disease
Multiple Myeloma
Rhabdomyolisis
Unfortunately, if you have had lab work over a period of several months that consistently shows your creatinine and BUN elevated and your eGFR decreased then there is no doubt that you have something going on with your kidneys. Especially if you have blood and protein in your urine. It is definately something that needs to be taken seriously and that needs to be investigated further to determine what the underlying problem is. Here is the link that talks about all the different causes of kidney disease, maybe this will help: http://www.medicinenet.com/kidney_failure/article.htm
Tami