Introduction Baseline data from Longitudinal Study of Adults Health (ELSA—Brasil), a cohort that investigates incidence and predictors of chronic diseases among 15 000 civil servants aged 35–74 years from six universities in Brazil, was fully accomplished in December 2010. From now on, main challenges are: avoid loss to follow-up over time, correct identification, and classification of incident outcomes.

Methods Follow-up data collection relies on annual phone interview to identify hospitalisations and emergency department visits, 3-year examination in research centres, spontaneous participant report and linkage with available databases from human resources department of universities and death certificates. Events of interest include: acute myocardial infarction, unstable angina, heart failure, peripheral artery disease, myocardial revascularisation, resuscitated sudden death, stroke, transient ischaemic attack, incident diabetes, diabetes related complications, chronic kidney disease, cancer and all-causes mortality. Besides, intermediate outcomes such as hypertension, obesity, cognitive decline, kidney and endothelial dysfunction will be ascertained. To guarantee the uniformity of the assessment, an ELSA Outcome Committee performs a reiterated verification of the protocols, scripts and certifies periodically researchers which are in direct contact with the population under study. The Morbidity and Mortality Committee aggregates specialists from the six research centres, in order to perform events classification according to standardised protocols.

Conclusions The great number of exposures studied will allow investigate many associations with outcomes of interest. Besides that, a promising issue of this study is the biological samples and DNA bank of all participants which will also allow nested case-control analysis.