There were 103,702 people living on the islands in March 2011, up 4% from 99,739 ten years earlier.
The islands population made up 2% of the national population in 2011 but the growth has not been uniform, with some islands seeing a large increase while others, including Arran, Bute and Islay, experienced a drop in population.
The figures are from the latest publication of the 2011 census from the National Records of Scotland (NRS).
The 2011 level is not a record high, with the population on the islands thought to have been larger at the start of the 20th century.
The most populated island area in 2011 was Lewis and Harris with 21,031 residents, an increase of about 5.5% since 2001.
In total, 50 islands saw an increase in population, with the largest increase in the Orkney Islands Council, which grew by 11%, 2,104 people, accounting for more than half of the increase across all the Scottish islands.
Three islands which were uninhabited in 2001 had residents in 2011 but the population of 43 islands fell over the decade.
Registrar General Tim Ellis said: "The population of the Scottish islands has increased over the last 10 years, however much of this increase is a result of the sizable population increases in Orkney, Shetland and the Western Isles.
"Some of the other larger islands such as Bute, Arran and Islay have seen population decrease over the decade."
The 2011 census recorded Scotland's population at 5.2 million.