Environment commissioner Karmenu Vella said: "The member states referred to the court today have received sufficient "last chances" over the last decade to improve the situation".
France, Germany, and Britain will be taken to court over their failure to respect limits for nitrogen dioxide (NO2), while Hungary, Italy, and Romania failed to meet required standards on the level of particulate matter.
Air pollution from NO2 causes an estimated 23,500 early deaths every year in the UK.
"The UK needs a new Clean Air Act fit for the 21st Century and targeted action, like scrappage schemes and clean air zones which keep the dirtiest vehicles out of our most polluted towns and cities".
Mr Vella said: "The decision to refer member states to the Court of Justice of the EU has been taken on behalf of Europeans". Air pollution requires urgent action and it's been clear for too many years that authorities all across Europe are failing to protect their people from illegal and harmful levels of air pollution.
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Levels of nitrogen dioxide, mostly produced by diesel vehicles, have been illegally high since 2010 in the vast majority of urban areas in the UK. "We will shortly build on our £3.5bn plan to tackle roadside emissions with a comprehensive clean air strategy". The problem was declared a public health emergency by a cross-party committee of MPs in 2016.
In a statement sent to Post&Parcel, ClientEarth's CEO James Thornton said: "On top of our three successful cases, today's legal action from the European Commission is more damning evidence of the mountain the United Kingdom government still has to climb to bring air pollution to within legal limits".
The European legal case now moves to the ECJ, which will hold a hearing within months. But Vella also admitted that "legal action alone will not solve the problem". If it does not, the court can then impose large fines.
The European Commission's chief Brexit negotiator said in order for a trade deal to be signed Britain would have to continue to comply with the EU's environmental regulations.
The Commission is also issuing additional letters of formal notice to Germany, Italy, Luxembourg, and the United Kingdom on grounds that they have disregarded European Union vehicle-type approval rules.
Reacting to the announcement, ClientEarth lawyer Ugo Taddei said: "We are glad that, at last, the Commission is taking serious steps to fight air pollution before the Court of Justice".