To understand the implications of Brexit for fundamental rights protection, it is important to distinguish between two legal Europes. Europe’s primary rights regime is the European Convention on Human Rights (ECHR), a treaty drawn up by the Council of Europe, which is an older organisation than the EU with a much wider membership.

The UK ratified the ECHR in 1951 and, since 1966, UK citizens have been able to take cases to the European Court of Human Rights (ECtHR) in Strasbourg. In 1998, the ECHR was incorporated into the UK’s legal systems by the Human Rights Act (HRA) and the devolution statutes, thereby enabling Convention rights to be enforced in UK courts as well.

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The Convention is distinct from the EU’s Charter of Fundamental Rights – of which more shortly – which relates to the actions of EU institutions and of member states in areas governed by EU law, and which is enforced by the European Court of Justice (ECJ) in Luxembourg, as well as by domestic courts.

There is an unfortunate tendency in the media and political debates to conflate the ECHR and the EU. For instance, the Vote Leave campaign’s website claims that “EU judges have … overruled UK laws on issues like … whether prisoners should be allowed to vote”. But it was, the ECtHR, not the ECJ which ruled, in 2005, that the UK’s blanket ban on prisoner voting breached the Convention and the ban remains in place.

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If the UK leaves the EU, this will have no direct effect on our obligations under the ECHR or domestic human rights statutes. People will still be able to rely on Convention rights before the UK and Strasbourg courts. But the separate protection for fundamental rights provided under EU law will no longer be available.

Fundamental rights were first recognised by the ECJ as forming an integral part of EU law in the 1970s and, today, respect for human rights is recognised to be one of the EU’s founding values. States wishing to join the EU must demonstrate a high standard of human rights protection, which in practice means that they must be signatories to the ECHR.

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In 2000, the EU took an important step to increase the visibility of human rights by adopting its own Charter of Fundamental Rights. Initially just a declaratory statement, the 2009 Lisbon Treaty gave it equal status with the other EU Treaties. The content of the charter overlaps with, but is much broader than, the ECHR. In particular, it includes various social and economic rights and gives much stronger protection to equality rights.

Controversy over the charter dates back to the Lisbon Treaty, when the UK negotiated a protocol declaring that it did not extend the powers of the British courts or the ECJ to enforce charter rights. However, this so-called "opt-out" has proved to be weaker than was claimed. This has lead Conservative politicians on both sides of the Brexit debate to criticise the charter, notably Michael Gove, who included it among his reasons for wishing to leave the EU and David Cameron who promised in 2015 to "make it explicit to our courts that they cannot use the EU Charter as the basis for any new legal challenge citing spurious new human rights grounds".

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Critics of EU fundamental rights law raise two main objections. First, there are concerns about the transfer of sovereignty from the UK to the EU and about loss of democratic accountability due to the increased power of judges to make decisions about rights. Whereas the HRA was carefully crafted to strike a balance between increased rights protection and preservation of the ultimate sovereignty of the UK Parliament, the ability to bring rights claims under EU law disturbs that constitutional equilibrium, since all domestic law which breaches EU law is invalid.

The second objection to EU fundamental rights law is more technical, namely that it confuses the protection of human rights at national level. Different human rights regimes apply depending upon whether issues are governed by EU law or purely by domestic law, which can create anomalies.

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So what would be the implications of Brexit for fundamental rights protection in the UK? It would undoubtedly reduce the opportunities for challenging government decisions and legislation on human rights grounds and the remedies available for rights breaches, as well as the range of rights which may be relied upon. Both the UK and Scottish parliaments would thereby gain more freedom to determine for themselves which, and how best, rights should be protected.

Brexit could also have an indirect effect on rights protection under the ECHR. It would remove an obstacle to withdrawal from the ECHR, and might embolden the UK Government to press ahead with plans to replace the HRA with a British Bill of Rights.

Whether this would lead to better or worse rights protection is a matter of judgment. All human rights regimes involve sometimes controversial value choices. For instance, while right-wingers tend to criticise the EU for excessive protection of social rights, left-wingers often argue that it gives too much weight to economic interests. Ultimately the answer depends on who one trusts to make better decisions about rights most of the time: EU or UK courts; judges or politicians?

Aileen McHarg is Professor of Public Law in the University of Strathclyde. A longer version of this article appears in the free e-book: Britain’s Decision: Facts and Impartial Analysis for the EU referendum.