According to a new Yale University study, the physical stress of running a marathon can cause short-term kidney injury.

Your muscles aren't the only things that hurt after running a marathon; your kidneys do too.

A US study has found the physical stress of running a marathon can cause short-term kidney injury.

Although the organs recover within two days after the race, the study does raise questions concerning potential long-term impacts of this strenuous activity at a time when marathons are increasing in popularity, say the researchers from Yale University.

"The kidney responds to the physical stress of marathon running as if it's injured, in a way that's similar to what happens in hospitalised patients when the kidney is affected by medical and surgical complications," said lead researcher professor of medicine Chirag Parikh Parikh.

Millions of people, including Australians, participate in marathons every year.

To investigate the effects of marathon running on kidney health, Prof Parikh and his team analysed blood and urine samples collected before the 42-kilometre 2015 Hartford Marathon.

They analysed a variety of markers of kidney injury, including serum creatinine levels, kidney cells on microscopy, and proteins in urine.

The researchers found that 82 per cent of the runners who were studied showed Stage 1 Acute Kidney Injury (AKI) soon after the race.

AKI is a condition in which the kidneys fail to filter waste from the blood.

The theory is that the potential causes of the kidney damage could be the result of a sustained rise in core body temperature, dehydration, or decreased blood flow to the kidneys that occur during a marathon.

"We need to investigate this further," said Prof Parikh. "Research has shown there are also changes in heart function associated with marathon running. Our study adds to the story - even the kidney responds to marathon-related stress."

The study has been published in the American Journal of Kidney Diseases.