Background: Intensive interventions on smoking cessation increase abstinence rates. However, few electronic mail (E-mail) based intensive interventions have been tested in smokers and none in primary care (PC) setting. The aim of the present study is to evaluate the effectiveness of an intensive E-mail based intervention in smokers attending PC services. Methods/design: Randomized Controlled Multicentric Trial. Study population: 1060 smokers aged between 18-70 years from Catalonia, Salamanca and Aragón (Spain) who have and check regularly an E-mail account. Patients will be randomly assigned to control or intervention group. Intervention: Six phase intensive intervention with two face to face interviews and four automatically created and personal E-mail patients tracking, if needed other E-mail contacts will be made. Control group will receive a brief advice on smoking cessation. Outcome measures: Will be measured at 6 and 12 months after intervention: self reported continuous abstinence (confirmed by cooximetry), point prevalence abstinence, tobacco consumption, evolution of stage according to Prochaska and DiClemente's Stages of Change Model, length of visit, costs for the patient to access Primary Care Center. Statistical analysis: Descriptive and logistic and Poisson regression analysis under the intention to treat basis using SPSS v.17. Discussion: The proposed intervention is an E-mail based intensive intervention in smokers attending primary care. Positive results could be useful to demonstrate a higher percentage of short and long-term abstinence among smokers attended in PC in Spain who regularly use E-mail. Furthermore, this intervention could be helpful in all health services to help smokers to quit. Trial Registration: Clinical Trials.gov Identifier: NCT01494246.