Background <p>Annual flu vaccination is recommended for children with rheumatic diseases. We investigated the cellular and humoral immune response and safety in pediatric patients that received inactivated influenza vaccines.</p> Methods <p>This is a comparative study of in 41 children with juvenile idiopathic arthritis (JIA) receiving influenza vaccination while being treated with methotrexate (MTX) or biological therapy. The influenza vaccination was administered as a single dose of trivalent influenza vaccine (TIV). Serological tests to monitor seroconversion and seroprotection were performed at baseline and at 4 as well as 12 weeks after vaccination.</p> Results <p>In all of the 41 children with JIA and the 22 healthy children seroconversion and seroprotection were observed for Influenza A. For Influenza B, no adequate seroconversion rates were not detected in any of the groups studied. No significant differences were observed in lymphocyte subpopulations when analysing time points and groups simultaneously. There were no relapses or cases of influenza infection after the vaccination. Our findings do not suggest non-specific immune activation following vaccination based on the distribution and quantity of the lymphocyte subsets that were investigated.</p> Conclusion <p>The present study demonstrates adequate seroprotection rates against influenza A in immunosuppressed children with JIA. The trivalent vaccine had good immunogenicity and was safe to use in both JIA treatment groups.</p>