Immune responses to neuronal proteins are a frequent occurrence in neurodegenerative diseases. This study determines the occurrence of autoantibodies to the three neurofilament subunits in phosphorylated and dephosphorylated forms and relates these measures to age, human leukocyte antigen (HLA), and severity of disease in Down syndrome (DS). IgG-type antibodies to three neurofilament (NF) subunits, NF-L, NF-M, and NF-H, in both phosphorylated and dephosphorylated forms were tested by immunoblot in 128 patients with DS and compared to antibody levels in 94 normal controls. DS was revealed by karyotype analysis. Antibodies to dephospho-NF-M, NF-M, and NF-L were more common in DS samples than in controls. Total pools of DS and control samples had similar frequency of antibodies to NF-H, but there was a higher prevalence of antibodies against NF-H in DS patients with moderate or mild disability (43.0%) compared with those having serious disability (14.3%). No NF-H antibody was seen among young children (age 14 years or younger) of the latter group. The HLA-DR15 allele was negatively correlated with antibodies against NF-H. The high prevalence of antibodies to neurofilament proteins and the differences between DS and control samples may reflect the cross-talk between neural and immune systems that could have an important role in defending neural structures from neurodegenerative processes. In children with DS the presence of antibodies to NF-H might reflect a more favorable prognosis.