The news comes just weeks after a Dutch trial using the friendly bacteria on pancreatitis sufferers led to the death of 24 people.
Brighton and Sussex University Hospitals NHS Trust are trialing the pots on wards at the Royal Sussex County Hospital in Brighton and the Princess Royal Hospital in Haywards Heath, which have had higher cases of Clostridium difficile infection.
The Trust said there has been science to support the use of probiotics, and said the yoghurt helps balance the bacteria in the stomach which could help make patients less susceptible to infection.
A spokesperson told NutraIngredients.com: "My understanding is that there has been no scientific evidence to suggest it could do any harm."
Medical director Matthew Fletcher said: "We are providing Actimel probiotic yoghurt to patients on the wards where we have previously had more cases of C.diff.
"There is some evidence to suggest that using these probiotics may reduce a patient's risk of C.diff
and we will be evaluating the difference this has made to the number of cases."
The trial is expected to last another three months.
Earlier this month it was revealed that 24 people died after being given probiotics to treat acute pancreatitis in a study organized by the University Medical Centre in Utrecht, Holland.
The Dutch Food and Consumer Product Safety Authority (VWA) has said there is no danger in taking probiotic dairy drinks - but is planning to release details on possible consequence of the bacteria on vulnerable groups.
Infection Clostridium difficile can cause diarrhoea and in severe conditions it can be fatal.
According to data handed to the Health Protection Agency, the number of reports increased from less than 1,000 in the early 1990s to 22,000 in 2002, 28,000 in 2003 and 44,488 in 2004 in the UK.
There have been studies which have suggested probiotics might help reduce superbug infection.
Probiotic-containing drinks may help reduce diarrhoea among older people receiving antibiotics, a study last summer found.
Mary Hickson from Imperial College, London, writing in the British Medical Journal , said hospital-bound elderly patients receiving antibiotics experienced 22 per cent less cases of diarrhoea if taking probiotic drinks.
According to the researchers, this prevention could lead to significant savings compared to standard treatment.
"The cost to prevent one case [using probiotics] would therefore be £50 (€74; $100) for antibiotic associated diarrhoea and £60 (€89; $120) for C difficile associated diarrhoea, excluding dispensing and nursing costs," wrote the researchers.
"Evidence suggests that additional treatment costs per patient for C difficile associated diarrhoea are on average $3669 (£1835, €2738) in the United States and £4000 (€5920, $8000) in the United Kingdom, mainly because of increased length of stay in hospital but also because of the use of vancomycin.
"Clearly substantial savings could be made by the routine use of probiotics," they state.