A Chicago Tribune investigation showed high levels of diesel soot in the air.
At Friday's board meeting, Metra announced it will switch to cleaner fuel for its locomotives and install more efficient air filters on its train cars.
Metra's own testing showed the highest levels of soot are in the first car behind the locomotive and they fall below current standards.
Also Friday, Metra reported trains in 2010 were on time 95.9 percent of the time. That's a slight improvement from 2009. The agency also says it's getting positive feedback on its new "quiet cars" program.