The report shows 16 incidents of crimes against birds of prey in the Borders last year, inculding the poisoning of a female golden eagle. The only region in Scotland with more reported incidents was the Highlands with 22.
In the whole of the UK, only three regions had a worse bird of prey crime rate than the Borders - one of them being Northumberland, also with 22.
In total, 20 birds in the Borders suffered due to wildlife crimes - which includes shootings, nest destruction and poisoning - making the Borders the third worst overall in Scotland behind the Highlands (24) and Aberdeenshire (23). Overall in the UK, crimes against bird of prey rose 40%.
Of the 20 incidents reported in the Scottish Borders, 13 involved the use of poison. Nine of the poison victims were buzzards, all of which involved the use of carbofurban. This includes six buzzards killed from March to September last year around Greenlaw.
But Bob Elliot, RSPB Scotland's Head of Investigations, said the high number of crimes against buzzards was due to their larger numbers in Scotland rather than the birds being specifically targeted.
However, he did admit that the Borders had a problem, which is likely to be bigger still with many crimes in rural areas going undetected.
"Buzzards are numerically far more than say eagles - that is why there are more crimes, said Mr Elliot.
"They are going well on the farmland areas but you find that when the young buzzards leave the nest some people think there are 'too many' in the area and persecute them.
"The Borders is one of the areas of concern. You tend to find these incidents are in remote areas where the public and police happen on it by accident.
"There is probably far, far more of these things going on."
The RSPB report highlights the case of the golden eagle death in August 2007, describing the Borders as a 'black hole' for breeding of the bird in Scotland.
The report adds: "Sadly, illegal persecution of birds of prey continues to be a shameful fact in parts of Scotland in the 21st century."
Mr Elliot said: "Scotland has its fair share of bad stuff that goes on as we have a lot of rare species.
"It is ridiculous that trappings and shootings of birds are happening still in 2008 - it has got to stop."
Mr Elliot added it was "very difficult" to tell if 2008 would see a rise or fall in reported incidents against birds of prey, although the Borders and Berwickshire specifically has had some high profile cases.
This includes a red kite being shot dead in Berwickshire in June, which was described by Mike Flynn, Scottish Society for the Prevention of Cruelty to Animals (SSPCA) Superintendent, as a "pointless and senseless killing."