Gonorrheal infection is generally limited to superficial mucosal surfaces lined with columnar epithelium. The areas most frequently involved are the urethra, cervix, rectum, pharynx, and conjunctiva. Squamous epithelium, which lines the adult vagina, is not susceptible to infection by the N. gonorrhoeae. However, the prepubescent vaginal epithelium, which has not been keratinized under the influence of estrogen, may be infected. Hence, gonorrhea in young girls may present as vulvovaginitis. Mucosal infections are usually characterized by a purulent discharge.

Uncomplicated gonorrhea in the adult male is an inflammatory and pyogenic infection of the mucous membranes of the anterior urethra. The most common symptom is a discharge that may range from a scanty, clear or cloudy fluid to one that is copious and purulent. Dysuria (difficulty in urination) is often present. Inflammation of the urethral tissues results in the characteristic redness, swelling, heat, and pain in the region. There is intense burning and pain upon urination.

Endocervical infection is the most common form of uncomplicated gonorrhea in women. Such infections are usually characterized by vaginal discharge and sometimes by dysuria. About 50% of women with cervical infections are asymptomatic. Asymptomatic infections occur in males, as well. Males with asymptomatic urethritis are an important reservoir for transmission and are at increased risk for developing complications. Asymptomatic males and females are a major problem as unrecognized carriers of the disease.  In the United States alone, according to the Centers for Disease Control and Prevention, the number of cases is estimated at about 700,000 a year.

In the male, the organism may invade the prostate resulting in prostatitis, or extend to the testicles resulting in orchitis. In the female, cervical involvement may extend through the uterus to the fallopian tubes resulting in salpingitis, or to the ovaries resulting in ovaritis. As many as 15% of women with uncomplicated cervical infections may develop pelvic inflammatory disease (PID). The involvement of testicles, fallopian tubes or ovaries may result in sterility. Occasionally, disseminated infections occur. The most common forms of disseminated infections are a dermatitis-arthritis syndrome, endocarditis and meningitis.

Rectal infections (proctitis) with N. gonorrhoeae occur in about one-third of women with cervical infection. They most often result from autoinoculation with cervical discharge and are rarely symptomatic. Rectal infections in men that have sex with men usually result from anal intercourse and are more often symptomatic. Partners must be treated as well to avoid reinfection.

Ocular infections by N. gonorrhoeae can have serious consequences of corneal scarring or perforation. Ocular infections (ophthalmia neonatorum) occur most commonly in newborns who are exposed to infected secretions in the birth canal. Part of the intent in adding silver nitrate or an antibiotic to the eyes of the newborn is to prevent ocular infection by N. gonorrhoeae.

Most of the information on bacterial invasion comes from studies with tissue culture cells and human fallopian tube organ culture. After the bacteria attach to the nonciliated epithelial cells of the fallopian tube, they are surrounded by the microvilli, which draw them to the surface of the mucosal cell. The bacteria enter the epithelial cells by a process called parasite-directed endocytosis. During endocytosis the membrane of the mucosal cell retracts and pinches off a membrane-bound vacuole (phagosome) that contains the bacteria. The vacuole is transported to the base of the cell, where the bacteria are released by exocytosis into the subepithelial tissue. The neisseriae are not destroyed within the endocytic vacuole, but it is not clear whether they actually replicate in the vacuoles as intracellular parasites.

A major porin protein, P.I (Por), in the outer membrane of the bacterium is thought to be the invasin that mediates penetration of a host cell. Each N. gonorrhoeae strain expresses only one type of Por; however, there are several variations of Por that partly account for different antigenic types of the bacterium.

Neisseria gonorrhoeae can produce one or several outer membrane proteins called Opa (P.II) proteins . These proteins are subject to phase variation and are usually found on cells from colonies possessing a unique opaque phenotype called O+. At any particular time, the bacterium may express zero, one, or several different Opa proteins, and each strain has 10 or more genes for different Opas.

Rmp (P.III) is an outer membrane protein found in all strains of N. gonorrhoeae. It does not undergo antigenic variation and is found in a complex with Por and LOS. It shares partial homology with the OmpA protein of Escherichia coli. Antibodies to Rmp, induced either by a neisserial infection or by colonization with E. coli, tend to block bactericidal antibodies directed against Por and LOS. In fact, anti-Rmp antibodies may increase susceptibility to infection by N. gonorrhoeae.

During infection, bacterial lipooligosaccharide (LOS) and peptidoglycan are released by autolysis of cells. Both LOS and peptidoglycan activate the host alternative complement pathway, while LOS also stimulates the production of tumor necrosis factor (TNF) that causes cell damage. Neutrophils are immediately attracted to the site and feed on the bacteria. For unknown reasons, many gonococci are able to survive inside of the phagocytes, at least until the neutrophils themselves die and release the ingested bacteria.

Neisserial LOS has a profound effect on the virulence and pathogenesis of N. gonorrhoeae. The bacteria can express several antigenic types of LOS and can alter the type of LOS they express by some unknown mechanism. Gonococcal LOS produces mucosal damage in fallopian tube organ cultures and brings about the release of enzymes, such as proteases and phospholipases, that may be important in pathogenesis. Thus, gonococcal LOS appears to have an indirect role in mediating tissue damage. Gonococcal LOS is also involved in the resistance of N. gonorrhoeae to the bactericidal activity of normal human serum. Specific LOS oligosaccharide types are known to be associated with  serum-resistant phenotypes of N. gonorrhoeae.

N. gonorrhoeae can utilize host-derived N-acetylneuraminic acid (sialic acid) to sialylate the oligosaccharide component of its LOS, converting a serum-sensitive organism to a serum-resistant one. Organisms with nonsialylated LOS are more invasive than those with sialylated LOS but organisms with sialylated LOS are more resistant to bactericidal effects of serum. There is also antigenic similarity between neisserial LOS and antigens present on human erthyrocytes. This similarity to "self" may preclude an effective immune response to these LOS antigens by maintaining the immunotolerance of the host.

N. gonorrhoeae is highly efficient at utilizing transferrin-bound iron for in vitro growth; many strains can also utilize lactoferrin-bound iron. The bacteria bind only human transferrin and lactoferrin. This specificity is thought to be, in part,  the reason these bacteria are exclusively human pathogens.

Strains of N. gonorrhoeae produce two distinct extracellular IgA1 proteases which cleave the heavy chain of the human immunoglobulin at different points within the hinge region. Split products of IgA1 have been found in the genital secretions of women with gonorrhea, suggesting that the bacterial IgA1 protease is present and active during genital infection. It is thought that the Fab fragments of IgA1 may bind to the bacterial cell surface and block the Fc-mediated functions other immunoglobulins.

Occasionally, as described above, invading Neisseria gonorrhoeae enter the bloodstream causing a Gram-negative bacteremia which may lead to a disseminated bacterial infection. Asymptomatic infections of the urethra or cervix usually serve as focal sources for bacteremia. Strains of N. gonorrhoeae that cause disseminated infections are usually resistant to complement and the serum bactericidal reaction. This accounts for their ability to persist during bacteremia. In Gram-negative bacteremias of this sort, the effect of bacterial endotoxin can be exacerbated by the lyis of bacterial cells which may simply liberate soluble LOS.