Systemic lupus erythematosus (SLE) is a complex autoimmune disease. Genome-wide linkage studies implicated a region containing the adhesion molecule P-Selectin. This family-based study revealed two regions of association within
P-Selectin
. The strongest signal, from a 21.4-kb risk haplotype, stretched from the promoter into the first two consensus repeat (CR) regions (
P
=8 × 10
−4
), with a second association from a 14.6-kb protective haplotype covering CR 2–9 (
P
=0.0198). The risk haplotype is tagged by the rare C allele of rs3753306, which disrupts the binding site of the trans-activating transcription factor
HNF-1
. One other variant (rs3917687) on the risk haplotype was significant after permutation (
P
10000
<1 × 10
−5
), replicated in independent pseudo case-control analysis and was significant by meta-analysis (
P
=
4.37
× 10
−6
). A third associated variant on the risk haplotype (rs3917657) replicated in 306 US SLE families and was significant in a joint UK-SLE data set after permutation. The protective haplotype is tagged by rs6133 (a non-synonymous variant in CR8 (
P
=9.00 × 10
−4
), which also shows association in the pseudo case-control analysis (
P
=1.09 × 10
−3
) and may contribute to another signal in
P-Selectin
. We propose that polymorphism in the upstream region may reduce expression of P-Selectin, the mechanism by which this promotes autoimmunity is unknown, although it may reduce the production of regulatory T cells.