The 57-kb gonococcal genetic island (GGI) encodes a type IV secretion system (T4SS) that is found in most strains of N. gonorrhoeae . This T4SS functions to secrete single-stranded DNA that is active in natural transformation. The GGI has also been found in some strains of N. meningitidis . We screened 126 isolates of N. meningitidis and found the GGI in 17.5% of strains, with the prevalence varying widely among serogroups. The GGI is found in a significant number of serogroup C, W-135, and X strains but was not found in strains of serogroup A, B, or Y. Through detailed PCR mapping and DNA sequencing, we identified five distinct GGI types in meningococci. DNA sequencing and a genetic assay revealed that the GGI was likely integrated into the meningococcal chromosome by the site-specific recombinase XerCD and that the GGI can be excised and lost from the genome. Functional studies showed that in contrast with the gonococcal T4SS, the meningococcal T4SS does not secrete DNA, nor does it confer Ton-independent intracellular survival. Deletion of T4SS genes did not affect association with or invasion of host cells. These results demonstrate that the GGI is found in a significant proportion of meningococcal strains and that while some strains carry multiple insertions and deletions in the GGI, other strains carry intact T4SS genes and may produce functional secretion systems.