Background: Alcohol is responsible for a large and growing proportion of the global burden of disease, as well as being the cause of social problems. Brief interventions are one component of comprehensive policy measures necessary to reduce these harms. Brief interventions increasingly take advantage of the Internet to reach large numbers of high risk groups such as students. The research literature on the efficacy and effectiveness of online interventions is developing rapidly. Although many studies show benefits in the form of reduced consumption, other intervention studies show no effects, for reasons that are unclear. Sweden became the first country in the world to implement a national system in which all university students are offered a brief online intervention via an e-mail. Methods/Design: This randomized controlled trial (RCT) aims to evaluate the effectiveness of this national system comprising a brief online intervention among university students who are hazardous and harmful drinkers. This study employs a conventional RCT design in which screening to determine eligibility precedes random allocation to immediate or delayed access to online intervention. The online intervention evaluated comprises three main components; assessment, normative feedback and advice on reducing drinking. Screening is confined to a single question in order to minimise assessment reactivity and to prevent contamination. Outcomes will be evaluated after 2 months, with total weekly alcohol consumption being the primary outcome measure. Invitations to participate are provided by e-mail to approximately 55,000 students in 9 Swedish universities. Discussion: This RCT evaluates routine service provision in Swedish universities via a delay in offer of intervention to the control group. It evaluates effects in the key population for whom this intervention has been designed. Study findings will inform the further development of the national service provision.