The European Commission will be attentive to anything that could "weaken dialogue and peace" in Northern Ireland, says its chief Brexit negotiator.
Michel Barnier singled out the decision to leave the customs union, which will mean some form of customs controls between NI and the Republic.
The UK and Irish governments have said they do not want customs posts.
But Ireland will have to agree customs arrangements with its EU partners.
Mr Barnier said Brexit had created uncertainty about the new borders of the EU.
He said the EU has had a role in supporting the Good Friday Agreement and would therefore be "particularly attentive... to the consequences of the UK's decision to leave the Customs Union."
Prime Minister Theresa May will officially notify the EU of the UK's intention to leave on 29 March.
A summit of EU member states will be held on 29 April to agree the guidelines for the EU's negotiating team which is headed by Mr Barnier.