During the Lisbon Referendum, some Anti-Lisbon groups (notably Coir) argued that the Treaty could lead to the European Court of Justice legalising abortion in Ireland - a view that wasn't shared by the Catholic Church, or some of the other anti-Lisbons groups. Nevertheless, Ireland will be seeking some form of guarantee that family law will not be affected by the Lisbon Treaty/the EU.
But now it appears that perhaps the anti-abortion groups have been focusing on the wrong European organisation - the European Court of Human Rights (which is under the Council of Europe, and not connected with the EU) is considering hearing a case concerning 3 women who claim that Ireland's abortion laws have breached their rights under the convention. Ireland's defense is mainly centred on the fact that the three women (known only as A, B and C) haven't exhaused the court system here (since the ECHR hsn't decided to hear the case yet). A, B and C contend that there is no point in going through the whole court system in Ireland since the whole thing is pretty much a foregone conclusion - one which would be very expensive for the women to go through to reach before going on to the ECHR anyway, and one which would have revealed their identities.
The Lithuanian government has sent submissions since one of the women is a Lithuanian based in Ireland. The Lithuanian government wants the ECHR to set out clearly the "minimum degree of protection" that the convention gives to women who want to have an abortion. The Lithuanian government also seems to side with the women's interpretation that they would be unlikely to be successful in the Irish court system, so they shouldn't be forced to go through the whole system before they reach the ECHR.
The Irish Times article on this has a good explaination, and it outlines the facts behind each woman.