Purpose The Mollerussa prospective cohort was created to study pre-diabetes in a population-based sample from the primary care setting in the semirural area of Pla d'Urgell in Catalonia (Spain). The aims of the study were to assess the prevalence of pre-diabetes in our population, the likelihood to develop overt diabetes over time and to identify risk factors associated with the progression of the condition. Participants The cohort includes 594 subjects randomly selected between March 2011 and July 2014 from our primary care population, who were older than 25 years, consented to participate and did not have a recorded diagnosis of diabetes. Findings to date At baseline, we performed a clinical interview to collect demographic, clinical and lifestyle (including a nutritional survey) characteristics; carotid ultrasound imaging to assess subclinical cardiovascular disease was also performed, and a blood sample was collected, with an overall <5% rate of missing data. An additional blood draw was performed 12 months after initial recruitment to reassess laboratory results in patients initially identified as having pre-diabetes, with an 89.6% retention rate. Several studies investigating various hypotheses are currently ongoing. Future plans All subjects recruited during the cohort creation will be followed long-term through annual extraction of data from health records stored in the electronic Clinical station in Primary Care database. The Mollerussa cohort will thus be a sound population-based sample for multiple future research projects to generate insights into the epidemiology and natural history of pre-diabetes in Spain.