The use of creatinine and cystatin C depends on the situation and the specific population being measured. Since cystatin C is produced in the entire body verses creatinine which is produced in skeletal muscles. It would be better to use cystatin C when looking at GFR with exercise since creatinine is a large marker of muscle damage and is biased. Impaired kidney function can be detected earlier in cystatin C compared with creatinine. Research is leaning more to using cystatin C instead of creatinine for estimating GFR. 

http://www.ncbi.nlm.nih.gov/pubmed/22732340

Thanks Forsse

My opinion is that eGFR is an initial screening tool independent of which method is used. Creatinine has been better characterized than cystatin C particularly as to its shortcomings. There are situations in which I would recommend against using creatinine, but that does not constitute a recommendation for using cystatin C. For example, after high does methotrexate, it would appear that muscle metabolism is suppressed, which can lead to normal creatinine plasma levels in patients with impaired renal function. I would think that in that situation, mGFR is preferred to obviate missing a morbidity.

My opinion is that eGFR is an initial screening tool independent of which method is used. Creatinine has been better characterized than cystatin C particularly as to its shortcomings. There are situations in which I would recommend against using creatinine, but that does not constitute a recommendation for using cystatin C. For example, high dose methotrexate, perhaps because muscle metabolism is suppressed, too often leads to normal creatinine plasma levels in patients with impaired renal function. I would think that for that situation, mGFR is preferred to obviate missing a morbidity, and in general for accurate assessment of current function and differences and trends for refining prognostication, mGFR is superior to eGFR. Sure eGFR gets a lot of use, but, it is not reliable.

Thanks for this significant contribution Carl A.W