Under the current system, if a male GP dies his widow will receive his pension entitlement based on all contributions made up to the point.
However, when a female GP leaves a widower, he will only be able to recieve payments based on contributions made after 1988.
This week, a judicial hearing, brought by the BMA, has begun in an attempt to solve the issue.
At the centre of the case is Iain Cockburn, the widower of GP Dr Clare Boothroyd.
A widow in Mr Cockburn’s situation would receive Ã‚Â£3,200 more in annual pension payments than he currently receives.
Writing in a blog post, BMA head of pensions Andy Blake said that the result of the case could have “potentially huge implications”, both for the NHS and other public sector pension schemes.
“A legal victory would also make it hard to justify the application of this regulation to unmarried partners including civil partners, to whom the pre-1988 rules also apply,” Mr Blake said.
Meanwhile, the health secretary Andrew Lansley argues that it would be too costly to government finances to correct the problem, with estimates suggesting it would cost around Ã‚Â£4 billion to eliminate the discrimination across all public sector pension schemes.
This is despite Alex Fox, one of the solicitors representing the BMA, revealing this week that the health secretary aknowledges that the current system is discriminatory.
Speaking to GPonline.com, Mr Fox said Mr Lansley has “accepted that this is direct discrimination”.
However he added that this does not necessarily mean that the government will lose the case if it can prove it still has a good cause not to let any changes in the legislation go ahead.
“The government “may still allow the act of discrimination to continue where it can justify that act,” said Mr Fox.