Congenital hypothyroidism (CH) is a heterogeneous disorder with largely unknown causes, affecting 1/3000-1/4000 new-borns. Individuals with Down syndrome have a much higher incidence of CH than the normal population, probably due to the extra copy of chromosome 21. Moreover, a girl has recently been described with CH and an interstitial deletion of proximal 21q, possibly revealing a recessive disease allele on the undeleted chromosome. To establish whether chromosome 21 is also involved in the etiology of familial cases of presumably autosomal recessive CH, we investigated 22 families with recessive CH, using 10 microsatellite markers from 21q. Linkage analysis allowing for heterogeneity revealed no signs of linkage even in a small proportion of the families, and two-point analysis of the markers made it possible to exclude the long arm of chromosome 21 from containing any major disease-causing gene.