Background: Multimorbidity is a major challenge for healthcare systems. However, currently, its magnitude and impact in healthcare expenditures is still mostly unknown. Objective: To present an overview of the prevalence and costs of multimorbidity by socioeconomic levels in the whole Basque population. Methods: We develop a cross-sectional analysis that includes all the inhabitants of the Basque Country (N = 2,262,698). We utilize data from primary health care electronic medical records, hospital admissions, and outpatient care databases, corresponding to a 4 year period. Multimorbidity was defined as the presence of two or more chronic diseases out of a list of 52 of the most important and common chronic conditions given in the literature. We also use socioeconomic and demographic variables such as age, sex, individual healthcare cost, and deprivation level. Predicted adjusted costs were obtained by log-gamma regression models. Results: Multimorbidity of chronic diseases was found among 23.61\% of the total Basque population and among 66.13\% of those older than 65 years. Multimorbid patients account for 63.55\% of total healthcare expenditures. Prevalence of multimorbidity is higher in the most deprived areas for all age and sex groups. The annual cost of healthcare per patient generated for any chronic disease depends on the number of coexisting comorbidities, and varies from 637 (sic) for the first pathology in average to 1,657 (sic) for the ninth one. Conclusion: Multimorbidity is very common for the Basque population and its prevalence rises in age, and unfavourable socioeconomic environment. The costs of care for chronic patients with several conditions cannot be described as the sum of their individual pathologies in average. They usually increase dramatically according to the number of comorbidities. Given the ageing population, multimorbidity and its consequences should be taken into account in healthcare policy, the organization of care and medical research.