In addition to the legal requirement to submit accurate Supplementary Declarations (SDs) within the prescribed deadlines, you must keep specific paperwork when completing and filing SDs.
You must retain a copy of every SD you submit - or an agent submits on your behalf - and all papers and documents used to compile your SDs for at least six years.
You can keep these documents in an electronic format, provided it can be read by HMRC.
HMRC carries out inspections from time to time to ensure that businesses are complying with their Intrastat obligations. The visit is almost always to your premises, even if you use an agent. When the HMRC representative visits, they'll need access to all your SD-related paperwork, so it's advisable to keep your records organised.
In most cases, managing your Intrastat responsibilities will be comparatively simple. It's prudent to check your SDs against your VAT return to see if the figures tally.
Any differences between your VAT returns and SDs may be queried by HMRC, although HMRC understands that circumstances - such as credit notes - may create a discrepancy between the SDs and the VAT return.
Check Notice 60, HMRC's guide to Intrastat - for more detailed guidance on inspections and day-to-day management of your Intrastat responsibilities. Read Notice 60 Intrastat general guide.