They believe athletes and their entourages as well as ticket holders may report symptoms of illness on social media before they seek any medical attention.
Members of the surveillance team at Health Protection Scotland (HPS) are going to search Twitter every hour during the Games looking for clusters of users reporting similar symptoms.
They believe the new approach may enable them to alert health boards to possible outbreaks of food poisoning or illness at an early stage, so services can respond rapidly if necessary.
Illnesses such as flu and the vomiting bug norovirus tend to be more common in the winter. While it is summer in Scotland, it is winter for some of the competing Commonwealth nations and people could travel to Scotland carrying bugs.
Any gathering where a large number of people come together also has the potential to aid the spread of germs.
Dr Jim McMenamin, a consultant epidemiologist for HPS, said his team would search one per cent of Twitter feeds posted in Scotland regularly during the Games using terms such as vomiting and diarrhoea, as well as common colloquialisms for such symptoms.
He said: "If we had a sudden increase in these terms without any linked media coverage and looked at the geographical location [of the Twitter users] and found they were coming from one particular bit of the country, that might serve as an early flag that there is something wrong that needs investigation.
"It means you can have a quick response time to limit the extent of that problem to the local community."
Arrangements are also in place so NHS 24 can report increases in people searching their website or calling their helpline about the same health problem, and data will be collected from GP surgeries and accident and emergency departments in the four health board areas hosting events.
Dr McMenamin said: "By far and away the biggest risk is from gastrointestinal illness, whether that is norovirus or food poisoning, followed by respiratory illness, whether that is cold or flu or other conditions."
NHS staff have also been alerted to look out for illnesses that do not spread in the UK such as malaria and viral haemorrhagic fevers.
Health Secretary Alex Neil, who visited HPS to discuss arrangements yesterday, said: "If someone from Sierra Leone is coming to the games and is carrying Ebola we are well prepared to be able to handle that."
Mr Neil said contingency plans were in place so that if extra hospital beds were required the health service could respond. He described the HPS arrangements as "the most advanced resilience plan for the Commonwealth Games" and said every possible technique and lesson from previous events had been learned.
In total 71 countries will be represented at the Games and 6500 athletes and team officials will live in the athletes' village. About one million tickets are expected to be sold for the different events and 15,000 volunteers will help the venues run smoothly.
Dr McMenamin said: "Looking at the experience of previous international gatherings such as the London Olympics, we know that the infectious disease challenge that they present is really very small. It is less than one per cent of the health-related attendances for care at any Games setting."
Foreign athletes and officials involved in the Games will be exempt from paying NHS charges if they become ill or are injured and need treatment during their visit to Scotland.
Public Health Minister Jane Ellison has signed off regulations laid before the UK Parliament to drop the charges for the Commonwealth Games Family - meaning those who are taking part or are involved - who need treatment between July 7 and August 7.