Two people have contracted a potentially deadly strain of E.coli and are being treated in hospital.
Five cases of the infection are being investigated but only two people have the O157 strain, NHS Orkney said.
The cases are not linked, according to the health board.
Dr Louise Wilson, director of public health for NHS Orkney, said: "The cases have occurred in two different areas of Orkney and there is no current indication that there is a link between the cases in these two areas.
"When we start an investigation it is not uncommon to find other people with symptoms or who are positive on testing.
"We are working closely with the environmental health team from OIC (Orkney Islands Council) to try and identify a source for the infections and the investigation is ongoing.
"E.coli O157 infections are often associated with environmental exposure but can also be food-related.
"One of the simplest things that can be done to prevent infection with E.coli O157 is to wash your hands thoroughly after using the toilet or changing nappies and before preparing or eating food. It is also important to wash your hands after contact with animals or their environment."
E.coli O157 is a bacterium which lives in the gut of animals such as cattle, sheep, deer and goats. It can also be carried by pets and wild birds.
In humans, the toxins that the O157 strain produces can cause diarrhoea and kidney failure as well as other illnesses. Young children and older people are said to be at the greatest risk.