The move follows a successful three-month trial in Surrey and Sussex last year, in which customers responded positively to the ban. The use of cheque books had fallen to account for only about 0.1 per cent of all purchases at the high street chain.
Other retailers are expected to follow Boots' move, as consumers increasingly use Chip and PIN cards.
An Alliance Boots spokesman said: 'Unfortunately, cheques still pose probably the highest risk of fraud to ourselves and our customers and because they are increasingly not used we have decided to phase them out completely.'
However, the retailer will make some exceptions: customers will still be able to pay for prescriptions and certain medical goods by cheque.
Petrol giant Shell stopped accepting cheques at its 586 UK outlets in 2005.
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