Objectives To compare healthcare costs and mortality rates of Dutch patients with a conventional (CON) general practitioner (GP) and patients with a GP who has additionally completed training in complementary and alternative medicine (CAM).Design - Comparative economic evaluation.Setting - Database from the Dutch insurance company Agis.Participants - 1 521 773 patients (98.8%) from a CON practice and 18 862 patients (1.2%) from a CAM practice.Main outcome measures - Annual information on five types of healthcare costs for the years 2006–2011: care by GP, hospital care, pharmaceutical care, paramedic care and care covered by supplementary insurance. Healthcare costs in the last year of life. Mortality rates.Results - The mean annual compulsory and supplementary healthcare costs of CON patients are respectively €1821 (95% CI 1813 to 1828) and €75.3 (95% CI 75.1 to 75.5). Compulsory healthcare costs of CAM patients are €225 (95% CI 169 to 281; p<0.001; 12.4%) lower and result mainly from lower hospital care costs (€165; 95% CI 118 to 212; p<0.001) and lower pharmaceutical care costs (€58; 95% CI 41 to 75; p<0.001), especially in the age categories 25–49 and 50–74 years. The costs in the last year of life of patients with CAM, GPs are €1161 (95% CI −138 to 2461; p<0.1) lower. This difference is entirely due to lower hospital costs (€1250; 95% CI 19 to 2481; p<0.05). The mean annual supplementary costs of CAM patients are €33 (95% CI 30 to 37; p<0.001; 44%) higher. CAM patients do not have lower or higher mortality rates than CON patients.Conclusions - Dutch patients whose GP additionally completed training in CAM on average have €192 (10.1%) lower annual total compulsory and supplementary healthcare costs and do not live longer or shorter than CON patients.