The move by unions, including UCU Scotland which represents 6000 academics, and the GMB, threatens significant disruption to universities.
In 2006, the last time Scottish lecturers took industrial action over pay, they refused to mark exam scripts, threatening the graduations of thousands of students.
The latest ballot follows the offer of a 1% pay rise for 2012/13 from the Universities and Colleges Employers Association (UCEA).
The offer is in response to a 7% pay claim by unions comprising an increase of 3.7% to keep salaries in line with inflation and a further rise of 3.3% to catch up with real terms pay cuts over the past three years.
UCEA, which negotiates on behalf of UK universities, believes the pay offer is the best available at a time of tight funding for institutions.
However, across the UK, unions believe universities have increased spending power due to the introduction of tuition fees of up to £9000 a year.
In Scotland, where fees are not charged to Scottish students, the UCU argues the last public funding settlement from the Scottish Government was large enough to allow for an improved pay offer.
The UCU said: "At this time of employment insecurity and increased pension contributions, staff are being expected to take home less pay, work longer hours, and accept workplace inequality and unfairness as a daily fact of life.
"UCU and the other higher education unions submitted a modest, reasonable and affordable claim to the employers for a pay offer to catch up with the cost of living and a living wage for support staff. Yet, all employers offered was another below-inflation pay offer and no meaningful action on any of our proposals to tackle the squeeze."
Sharon Holder, GMB national officer, said "GMB is recommending that members vote yes for strike action for three reasons.
"First, the offer goes nowhere to meet the claim for a 7% increase. Secondly, while university employers enjoy the benefits of a windfall increase in student fees they expect staff to deliver better services with no pay rise.
"Thirdly, due to inflation higher education staff continue to endure a real terms cut in living standards. This is just not fair."
A UCEA spokesman said: "The 1% offer has been made at a time when the UK higher education sector continues to face considerable financial uncertainties. Meeting the trade unions' pay claim of 7% would cost the sector in the region of £1bn. We hope trade union members will consider the wider situation facing their institution, their sector and their students as they decide on the most appropriate course of action."
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