The youngsters had both visited Colzium Park in Kilsyth, North Lanarkshire, shortly before becoming unwell.
NHS Lanarkshire's health protection team is working with North Lanarkshire Council and Health Protection Scotland to investigate the two cases of E.coli O157, both of which are children under the age of five.
One of the children has fully recovered and is at home while the other is receiving treatment in hospital
Dr Josephine Pravinkumar, consultant in Public Health Medicine with the health board, said: "We are currently investigating any potential common sources of exposure.
"People can become infected in a number of ways through eating contaminated food, contact with infected animals or animal faeces, contact with other people who have the illness or drinking contaminated water.
"Our initial investigations have found that both children visited Colzium Park in Kilsyth shortly before becoming unwell.
"However, investigations into other possible sources are continuing."