The pathophysiology of N gonorrhoeae and the relative virulence of different subtypes depend on the antigenic characteristics of the respective surface proteins. Certain subtypes are able to evade serum immune responses and are more likely to lead to disseminated (systemic) infection.
Well-characterized plasmids commonly carry antibiotic-resistance genes, most notably penicillinase. Plasmid and nonplasmid genes are transmitted freely between different subtypes. The ensuing exchange of surface protein genes results in high host susceptibility to reinfection. The exchange of antibiotic resistance genes has led to extremely high levels of resistance to beta-lactam antibiotics. Fluoroquinolone resistance has also been documented on multiple continents and in widespread populations within the United States. 
Infection of the lower genital tract, the most common clinical presentation, primarily manifests as male urethritis and female endocervicitis. Infection of the pharynx, rectum, and female urethra occur frequently but are more likely to be asymptomatic or minimally symptomatic. Retrograde spread of the organisms occurs in as many as 20% of women with cervicitis, often resulting in pelvic inflammatory disease (PID), with salpingitis, endometritis, and/or tubo-ovarian abscess. Retrograde spread can lead to frank abdominal peritonitis and to a perihepatitis known as Fitz-Hugh-Curtis syndrome.
Long-term sequelae of PID, such as tubal factor infertility, ectopic pregnancy, and chronic pain, may occur in up to 25% of affected patients. Epididymitis or epididymo-orchitis may occur in men after gonococcal urethritis. Lower genital infection is a risk factor for the presence of other sexually transmitted diseases (STDs), including human immunodeficiency virus (HIV).
Infertility in women:
Gonorrhea can spread into the uterus and fallopian tubes, causing pelvic inflammatory disease (PID). PID can result in scarring of the tubes, greater risk of pregnancy complications and infertility. PID requires immediate treatment.
Gonorrhea can cause a small, coiled tube in the rear portion of the testicles where the sperm ducts are located (epididymis) to become inflamed (epididymitis). Untreated epididymitis can lead to infertility.
- Infection that spreads to the joints and other areas of your body:
The bacterium that causes gonorrhea can spread through the bloodstream and infect other parts of your body, including your joints. Fever, rash, skin sores, joint pain, swelling and stiffness are possible results.
- Increased risk of HIV/AIDS:
Having gonorrhea makes you more susceptible to infection with human immunodeficiency virus (HIV), the virus that leads to AIDS. People who have both gonorrhea and HIV are able to pass both diseases more readily to their partners.
Babies who contract gonorrhea from their mothers during birth can develop blindness, sores on the scalp and infections.