British Journal of Sports Medicine study found taking probiotics more than halved the days they had symptoms. However, a British specialist said the same effect was less likely for people who were less active.
The small study conducted at the Australian Institute of Sport in Canberra focused on 20 top-level endurance runners during their intensive winter training programme, when colds and other respiratory infections can be disruptive.
Over the four months, all 20 received two month-long courses of pills - one containing the bacterium Lactobacillus fermentum, and the other containing no active ingredients.
All the athletes then recorded any days in which they were suffering from symptoms such as coughs and runny noses.
They then compared the toll of illness across the group, finding a total of 72 days in which people taking the "dummy" pills complained of symptoms.
When the same number of "probiotic" days was examined, only 30 were hit by illness.
Blood tests taken from the athletes found doubled levels of interferon gamma, a chemical involved in the body's immune system, suggesting that the probiotics might somehow be helping the body to protect itself.
There is increasing evidence that probiotic supplements - which contain so-called "friendly bacteria" - can have an effect on the immune system, although it is unclear precisely how.
Recent studies have found that even though the bacteria are vastly outnumbered by those already present in the gut, they appear to have an effect on the metabolism.
The researchers said that the reason behind the study was to find ways to maximise the benefits to athletes getting ready for major events.
"An improvement in resistance to common illnesses constitutes an important benefit to elite athletes undertaking high-level training in preparation for national and international competitions," they wrote.
However, they said that it would be worth investigating the potential of probiotics to help everyone else.