Brown said the book explored "certain aspects of Christian history"
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Best-selling novel The Da Vinci Code has been banned in Iran as a result of protests from Christian clergy.
Eight previous editions of the Persian translation of Dan Brown's book will remain in the country's shops but no further versions can be produced.
The Da Vinci Code has sold 40 million copies worldwide and was turned into a film, which was not released in Iran.
Some Christians objected to its theory that Jesus married Mary Magdalene, with their descendants surviving today.
There were protests in several countries when the movie was released in May, and it was banned in places such as the Philippines' capital Manila and some Indian states.
A spokesman for Iran's culture ministry said that "based on the request of three Christian clerics" they had "decided to ban its re-publication".
There are believed to be about 100,000 Christians in Iran, a nation of some 69 million Muslims.