Will HMRC penalise us?

My partner and I own two properties 50:50. We live in both properties and have never rented them out or used either to generate an income. We have just found out now that we should have registered one of them as our main residence. If we do this now, would we be penalised by HMRC?

Look at www.hmrc.gov.uk/manuals/cgmanual/CG64545.htm, where you can see that if the taxpayer did not make a valid election, then it is a matter of fact which property is the main residence for tax purposes. There is a list of criteria there to determine which house 'deserves' to get the relief. For example: (a) where does the taxpayer spend most of their time? (b) where is the taxpayer registered to vote, etc.?