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To determine whether vaccinations aggravate the course of autoimmune diseases such as juvenile idiopathic arthritis (JIA) and whether the immune response to vaccinations may be hampered by immunosuppressive therapy for the underlying disease.In this multicenter cohort study, 234 patients with JIA (ages 1–19 years) were vaccinated with meningococcal serogroup C (MenC) conjugate to protect against serogroup C disease (caused by Neisseria meningitidis). Patients were followed up for disease activity for 1 year, from 6 months before until 6 months after vaccination. IgG antibody titers against MenC polysaccharide and the tetanus carrier protein were determined by enzyme‐linked immunosorbent assay and toxin binding inhibition assay, respectively. A serum bactericidal assay was performed to determine the function of the anti‐MenC antibodies.No change in values for any of the 6 components of the core set criteria for juvenile arthritis disease activity was seen after MenC vaccination. Moreover, no increase in the frequency of disease relapse was detected. Mean anti‐MenC IgG concentrations in JIA patients rose significantly within 6–12 weeks after vaccination. Of 157 patients tested, 153 were able to mount anti‐MenC IgG serum levels >2 μg/ml, including patients receiving highly immunosuppressive medication. The 4 patients with a lower anti‐MenC antibody response displayed sufficient bactericidal activity despite receiving highly immunosuppressive medication.The MenC conjugate vaccine does not aggravate JIA disease activity or increase relapse frequency and results in adequate antibody levels, even in patients receiving highly immunosuppressive medication. Therefore, patients with JIA can be vaccinated safely and effectively with the MenC conjugate. [ABSTRACT FROM AUTHOR]