It has been reported that celiac disease (CD) is strongly associated with the HLA-DQ2 alleles DQA1*0501 and DQB1*0201. However, this association only accounts for a portion of the genetic component of CD. Several non-HLA loci and candidate genes that potentially contribute to CD susceptibility have been reported, but have not been confirmed. The aim of this study was to identify loci that contribute to disease susceptibility in a CD population from Finland. We performed a genomewide linkage scan and identified two regions of significant linkage to CD (6p and 2q23-32) and one region of suggestive linkage (10p). We also performed targeted typing and analyses that replicated the associations of the HLA and CTLA4 loci. © 2004 Wiley-Liss, Inc.