The interaction of the immune system with Neisseria commensals remains poorly understood. We have previously shown that phosphoethanolamine on the lipid A portion of lipooligosaccharide (LOS) plays an important role in Toll-like receptor 4 (TLR4) signaling. For pathogenic Neisseria, phosphoethanolamine is added to lipid A by the phosphoethanolamine transferase specific for lipid A, which is encoded by lptA. Here, we report that Southern hybridizations and bioinformatics analyses of genomic sequences from all eight commensal Neisseria species confirmed that lptA was absent in 15 of 17 strains examined but was present in N. lactamica. Mass spectrometry of lipid A and intact LOS revealed the lack of both pyrophosphorylation and phosphoethanolaminylation in lipid A of commensal species lacking lptA. Inflammatory signaling in human THP-1 monocytic cells was much greater with pathogenic than with commensal Neisseria strains that lacked lptA, and greater sensitivity to polymyxin B was consistent with the absence of phosphoethanolamine. Unlike the other commensals, whole bacteria of two N. lactamica commensal strains had low inflammatory potential, whereas their lipid A had high-level pyrophosphorylation and phosphoethanolaminylation and induced high-level inflammatory signaling, supporting previous studies indicating that this species uses mechanisms other than altering lipid A to support commensalism. A meningococcal lptA deletion mutant had reduced inflammatory potential, further illustrating the importance of lipid A pyrophosphorylation and phosphoethanolaminylation in the bioactivity of LOS. Overall, our results indicate that lack of pyrophosphorylation and phosphoethanolaminylation of lipid A contributes to the immune privilege of most commensal Neisseria strains by reducing the inflammatory potential of LOS.T he members of the genus Neisseria that colonize humans are classified into two pathogenic and eight commensal species. Infections due to the two pathogenic species, N. meningitidis and N. gonorrhoeae, represent a major public health problem around the world. N. meningitidis is the leading cause of epidemic meningitis, causing approximately 50,000 deaths worldwide each year (53). N. gonorrhoeae is a major cause of infections worldwide, estimated to be 60 million annually. In women, gonococcal infection can lead to pelvic inflammatory disease in 10 to 20% of those infected, causing chronic pain, infertility, and risk for ectopic pregnancy (22,42,50).Although it can be a deadly human pathogen, N. meningitidis is carried in the nasopharynx by approximately 10% of the population and only results in disease characterized by septicemia and meningitis at low frequencies (65). Asymptomatic carriage of N. meningitidis, which is infrequent in infancy and peaks in early adulthood, is the mechanism by which the reservoir of meningococci is maintained within the population. Similarly, asymptomatic gonococcal infection of women plays an important role in maintaining transmission of the organism (16).The eight commensal Nei...