National Trust rangers will carry out a survey of how many breeding pairs of the birds live on the habitat over the next three months.
The count takes place every five years. The last survey indicated numbers had fallen by a third.
Head ranger David Steel is hopeful of an increase this year but admitted cold weather could have had a negative impact on numbers.
"The extreme winds affected the their ability to feed as they made their way back to their summer breeding grounds," he said.
The 2008 survey recorded 36,835 pairs of puffins compared to the 55,674 pairs living on the islands in the 2003 census.
A team of 11 rangers will check thousands of burrows on the eight islands in search of nesting birds.
As well as the puffins, the islands host thousands of grey seals along with many other types of bird, including Arctic Terns, Guillemots and Razorbills.
Dozens of seabirds, including puffins, were washed up along the County Durham coast in March, with experts blaming weather conditions and a shortage of food.
