The purpose of this study was to investigate any association between IgA deficiency (IgAD) and juvenile rheumatoid arthritis (JRA) among Iranian children.This case-control study was carried out on 83 children who were diagnosed as JRA according to American College of Rheumatology (ACR) criteria; Patients were admitted at the rheumatology clinic of Children's Medical Center, (Tehran). Serum immunoglobulins concentrations were determined by nephelometry method. Control group was 112 healthy children who were matched for age and gender. Informed consent obtained from all parents.Selective IgA deficiency (sIgAD) was found only in a boy (1.2%) among JRA children; however, partial IgA deficiency was found in 6(7.1%) of patients with JRA and in 12(10.7%) of control subjects, this difference was not statistically significant (p=0.46). Immunoglobulins levels in patients with JRA (IgM: 126.7±57.2, IgG: 1182.3±351 and IgA:169.3±98) were significantly higher than their controls (IgM: 104±52, IgG:802±220 and IgA: 94.6±47) (p<0.05). Patients with growth failure had higher IgM, IgG and IgA levels in comparison with patients without growth failure; however, this difference was significant about IgM and IgG levels (p<0.05).In contrast to other similar studies, the number of IgAD did not differ significantly between JRA patients and their control counterpart; this might be partly due to the high rate of consanguineous marriages in Iran that resulted in increased prevalence of clinically undiagnosed partial IgAD in general population. Hence, future epidemiological studies are warranted to make it clear.