Tinsley and Brinsworth are said to be unlikely to meet new government targets on pollution levels due to be introduced in 2005.
The M1 has been blamed for the problem there and pollution experts who compiled the survey say the M1 is a "major source" of pollution in Rotherham.
They are calling for the Government to scrap plans to turn part of the motorway in South Yorkshire into a four-lane "super-highway" - and impose a 55mph speed limit instead.
Meanwhile the former mining community of Brampton Bierlow is also said to be unlikely to meet pollution targets.
Research has shown that Brampton's problems are being caused by many residents still burning solid fuel - some of it bought illegally from cowboy coal merchants - which doesn't come up to the required standard.
The M1 in South Yorkshire is said to be one of the busiest stretches of road outside London - and highways bosses say widening it will help tackle traffic snarl-ups.
But a working group set up by Rotherham Council says more research is needed on the effects of proposals to widen the motorway and how a 55mph zone could impact on air pollution.
They say extending South Yorkshire's Supertram network into Rotherham should also help to cut pollution, which it warns is a growing health risk.
And it wants to see more research carried out to determine how many people are suffering serious health problems as a result of air pollution.