Following is the list of top institutions in Scotland by region:

(1) Edinburgh:

Heriot-Watt University - Ranked 31st in the UK according to the Sunday Times University Guide 2012.

Edinburgh Napier University - Best modern university in Scotland by Guardian 2009.

Queen Margaret University - Awarded Queen's Anniversary Prize for research into the clinical applications of speech technology in 2002.

University of Edinburgh - 6th in the UK, 11th in Europe and 47th in the world by Newsweek 2006.

(2) Glasgow:

Glasgow Caledonian University - Winner of the Times Higher Education award for Outstanding Support for Overseas Students in 2008.

University of Glasgow - rated the best campus in Scotland and 3rd in the UK for overall student experience.

University of the West of Scotland - listed as the second most active knowledge transfer higher education institution in Scotland.

University of Strathclyde - ranked first in Scotland and 30th in the world by the Financial Times MBA league tables 2008.

(3) Other:

Robert Gordon University - Top university in Scotland for graduate employment and was ranked 10th in the U.K.

University of Aberdeen - Ranked 137th in THES-QS World Top 200 Universities Ranking 2007.

University of Dundee - Top 3 in Scotland for teaching and research. Rated in the Top 5 in UK by the National Audit Office.

University of St Andrews - Oldest university in the region and was rated top 5 in the United Kingdom.

University of Stirling - 37th in UK by the Times 2008.

University of Abertay Dundee - Ranked number one in the United Kingdom for its investment in information technology facilities (Financial Times 2002).

Top 5 Universities in Scotland by Complete University Guide 2009:
1 St Andrews
2 Glasgow
3 Edinburgh
4 Strathclyde
5 Stirling

Suggested Reading:

Top Law Schools in Scotland

Scottish University of the Year

Top Medical Schools in Scotland
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World University Ranking Tables

America - US News & World Report, The Princeton Review, BusinessWeek
Canada - Maclean's, Gourman Report Ranking of Canadian Universities
UK - Sunday Times, Guardian, Times Good University Guide, Daily Telegraph
World - Shanghai Jiao Tong ARWU Rankings, Webometrics, Newsweek