The study aims to give a picture of how the birds are faring across the UK after years of decline.
In Scotland, choughs are only found in a small area of the south-west, with 90% of them concentrated on the island of Islay where the population has struggled in recent years.
A drop in the survival of young birds led to the loss of 14 pairs - or 20 per cent of the island's population - between 2002 and 2012.
A team of surveyors has now begun work to chart the fortunes of the "acrobatic" birds, known for their striking red bill and legs and flamboyant flying style.
Researchers are particularly concerned about the survival rates of young birds in their first year. It is thought that variations in weather and food abundance could be having an impact on the survival of these sub-adult choughs.
The health of the island's coastal dune systems is a particularly important factor as they are vital foraging grounds for the birds.
RSPB research assistant Michal Sur walks up to 20km a day searching Islay's most remote areas for the birds.
He said: "The core of the population breeds in old buildings or farm sheds inland but choughs have also traditionally nested in caves along the coast.
"We have information on historical nest sites from previous surveys and are searching remote coastal areas in the north and east of Islay and try to find out whether any chough are using these inaccessible sites.
"Choughs are quite easily spotted because of their distinctive flying style but unfortunately they are becoming a far less common sight, even on the stronghold of Islay."
A member of the crow, or corvid, family, choughs primarily feed on insects and larvae and in particular those that are found in the dung of cattle.
The work on Islay is part of a national study to give a better picture of how the birds are coping across the UK.
The information gathered will help target conservation efforts for the recovery of the species in areas where it is in decline.
The 2014 survey on the island is a joint initiative between RSPB, SNH and the Scottish Chough Study Group, which has been monitoring the birds on Islay since the early 1980s.