The fall of 1.14% for Scottish companies compares with a rise of 20.28% over the year for the FTSE Aim all share index.
There were 24 Scottish companies on Aim for the whole of 2013 with a combined market capitalisation of £1714.55m at the end of 2013 compared with a combined market cap of £1734.38m at the end of 2012.
In preparing these figures, BDO has excluded two companies: Pinnacle which had a 1 for 100 share issue during the year and Superglass which switched to Aim from the main market.
The biggest increase in market cap was enjoyed by software services company Iomart which increased by £69.89m over the year followed by Smart Metering which rose by £54.64m and Craneware which increased by £31.44m.
The largest fallers were dating services firm Cupid which dropped £95.85m; oil services firm Bowleven which fell £89.1m; and oil services firm Lansdowne oil and gas which was down £46.35m.
Neil McGill, corporate finance director with BDO, said: "Scotland has a relatively shallow pool of AIM listed companies which always makes it difficult to identify trends from the overall change in the index but it is interesting to note the sectoral differences.
"Technology companies fared pretty well during the year with the ambitious and dynamic Iomart improving their value through some strategic and timely acquisitions. Equally Smart Metering and Craneware had an excellent year, growing their market cap substantially as a result."
There was always the possibility of volatility hitting the share prices of smaller oil and gas companies, he said, with them being hit by funding issues related to development costs on new fields.
He said: "The drop in equity valuations for Bowleven and Lansdowne impacted on the wider Scottish portfolio. Cupid was a significant faller due to some well publicised issues, however steps have been taken to focus on the core business after the sale of the casual dating business"
"With both Iomart and Smart Metering valued in excess of a quarter of a billion pounds it is an indication of both the quality of company on the market and how useful AIM listing can be for some businesses.
"It allows access to capital at a time when it may not be readily available elsewhere, and provides a platform to promote and publicise the activities of a business, whilst also lending credibility."
The number of firms listed on AIM increased in 2013 for the first time in six years with 69 flotations raising a total of £1.17bn which was the highest value raised in any year since 2008.Mr McGill added: "There are grounds for optimism that the markets are improving and AIM is returning in confidence as a useful and viable source of funding for the right type of business. I would expect more of the same during the coming year as business owners seek different means of funding for growth and expansion."