The genetic basis of complex (auto)immune diseases has been studied fo
r an ovine nematode infection, human rheumatoid arthritis (RA), early
onset pauciarticular arthritis (EOPA) and multiple sclerosis (MS). Imm
unoprinting combines the powerful simplicity of polymerase chain react
ion (PCR)-based amplification of discrete, highly informative microsat
ellite loci with the principle of genetic associations. This approach
has allowed us to define novel genetic risk factors in adult RA patien
t categories whereas EOPA forms in juveniles display other prominent g
enetic contributions. Differentially regulated tumor necrosis factor (
TNF) expression may lead to a better understanding of the causal patho
genesis of EOPA while T cell receptor (TCR) gene polymorphisms appear
crucial for RA manifestation in certain patient groups. Statistically
significant marker associations have still to be defined for MS in lar
ger panels of patient and control cohorts. The clinical course of the
disease will probably have to be taken into account when associations
with lymphokine levels are evaluated. In essence a convoluted myriad o
f negative and a few positive disease association data have been gener
ated efficiently by immunoprinting. As expected, the interrelationship
s are truly complicated between the polymorphic genetic instances pred
isposing to autoimmune disease. Nevertheless, risk factors may be defi
ned on an individualized basis by indirect gene diagnosis revealing pr
edispositions and providing a more solid basis for differential diagno
sis and treatment.