British researchers reviewed 12 studies involving nearly 800 children with eczema and found probiotics did nothing to ease itching and the rash.
And in separate studies 46 patients reported side effects including infection and bowel damage.
Experts said more trials were needed into the long-term safety of their use.
Eczema affects one in 20 people at some time in their lives and is increasingly common among children - a fifth of children in the UK now has eczema.
The causes are complex, but the finding that people with eczema have different bacteria in their guts from others has led to some doctors recommending probiotics to treat this skin problem.
Probiotics are naturally occurring microbes often found in the intestines of infants, but in recent years their natural occurrence has decreased, which may explain why there has been an increase in the prevalence of eczema.
But Dr Robert Boyle, of Imperial College London, and a researcher for the National Institute for Health Research (NIHR) who carried out the review for the Cochrane Collaboration, says, "There is no evidence that probiotics are a worthwhile treatment for eczema," and he said they may even be harmful for certain groups of people, such as very young infants or others susceptible to infection.
However, he said it was possible that new probiotics, yet to be studied, might have an effect.
And there is evidence emerging that probiotics might be useful for preventing eczema when taken during pregnancy or in the first weeks of life.
Professor Ashley Woodcock, of Manchester University, has been carrying out his own study into the effects of probiotics on eczema risk in infants.
He said: "We have no data on the long-term impact/safety on the use of probiotics in young children. Until that time, their use should be restricted to clinical trials which are properly designed, adequately powered and long enough to understand the long-term outcomes."
He said although eczema was increasingly common, existing treatments could make a huge difference to both the disease and the patient's quality of life, BBC reports.
Member of the British Association of Dermatologists Dr Nick Levell said: "There are many very well researched and effective treatments available for eczema, so sufferers should seek medical advice from their GP."