The lymphotoxin (LT) β receptor plays a critical role in secondary lymphoid organogenesis and the classical and alternative NF-κB pathways have been implicated in this process. IKKα is a key molecule for the activation of the alternative NF-κB pathway. However, its precise role and target genes in secondary lymphoid organogenesis remain unknown, particularly with regard to high endothelial venules (HEV). In this study, we show that IKKα AA mutant mice, who lack inducible kinase activity, have hypocellular lymph nodes (LN) and nasal-associated lymphoid (NALT) tissue characterized by marked defects in microarchitecture and HEV. In addition, IKKα AA LNs showed reduced lymphoid chemokine CCL19, CCL21, and CXCL13 expression. IKKα AA LN-and NALT-HEV were abnormal in appearance with reduced expression of peripheral node addressin (PNAd) explained by a severe reduction in the HEV-associated proteins, glycosylation-dependent cell adhesion molecule 1 (GlyCAM-1), and high endothelial cell sulfotransferase, a PNAd-generating enzyme that is a target of LTαβ. In this study, analysis of LTβ−/− mice identifies GlyCAM-1 as another LTβ-dependent gene. In contrast, TNFRI−/− mice, which lose classical NF-κB pathway activity but retain alternative NF-κB pathway activity, showed relatively normal GlyCAM-1 and HEC-6ST expression in LN-HEV. In addition, in this communication, it is demonstrated that LTβR is prominently expressed on LN-and NALT-HEV. Thus, these data reveal a critical role for IKKα in LN and NALT development, identify GlyCAM-1 and high endothelial cell sulfotransferase as new IKKα-dependent target genes, and suggest that LTβR signaling on HEV can regulate HEV-specific gene expression.