Rectal Reality Check: What Everyone Should Know About Anal STIs

Sexual health conversations usually focus on genital infections, but the health of the anus and rectum is just as important, especially for LGBTQ+ populations. Men who have sex with men (MSM), transgender, and nonbinary (TNB) individuals experience disproportionately high rates of sexually transmitted infections (STIs), many of which affect the rectum and anus.

These infections often fly under the radar because they may not cause noticeable symptoms. Other times, their signs can mimic more familiar gastrointestinal or hemorrhagic conditions, making them harder to detect. That’s why talking openly about anal sexual health with your provider and knowing what to look for is so important.

Understanding Incidence

STIs are not unique to LGBTQ+ populations – HIV, HPV, chlamydia, herpes, gonorrhea, syphilis, and the like can affect anyone. The difference is in where they show up, which changes how they’re detected and how they present.

Extragenital infections (those affecting the rectum and throat) are common among LGBTQ+ populations, yet despite higher rates, transgender and non-binary (TNB) individuals often receive less frequent extragenital testing than urogenital testing. This mismatch can leave infections undiagnosed – a study of 626 TNB patients found rectal chlamydia in 15% and rectal gonorrhea in 12%, while urogenital infections were far less common.¹

Among MSM, the lifetime risk of acquiring HIV is estimated at one in six, compared with one in 524 for heterosexual men.² Anal receptive intercourse can directly disrupt the mucosal lining of the anus and rectum, stripping away the naturally protective epithelial cell layers and mucous coating. Once this barrier is compromised, the disruption provides a pathway for pathogens (including bacteria, viruses, and parasites) to enter the body and, in some cases, the circulatory system.

Behavioral and social factors also influence infection risk. Multiple partners, condomless sex, chem sex (sex under the influence of recreational drugs), and oral-anal contact all increase the chance of exposure. Because rectal infections often produce no symptoms (about 85% in MSM), they can go unnoticed for months, increasing the risk of spreading infections to others.

When symptoms do appear, they can be subtle or resemble more common anorectal conditions. Rectal discharge, bleeding, pain during bowel movements, and anal ulcers may be mistaken for hemorrhoids, fissures, or even inflammatory bowel disease (IBD).

Treatment and Prevention Basics

STIs affecting the anus and rectum can be bacterial, viral, or parasitic.

Bacterial infections include gonorrhea, chlamydia, syphilis, Shigella, and Campylobacter. These infections are usually treatable with antibiotics, though antimicrobial resistance is an emerging concern, particularly with Shigella and gonococcal strains.2

Where these bacteria show up in the body can change how they appear. For example:

• Gonorrhea and chlamydia in the urogenital tract cause discharge, burning with urination, or pelvic pain. In the rectum, however, infections may produce very subtle or no symptoms at all. Some patients notice discharge, mild bleeding, or discomfort during bowel movements, but many have nothing noticeable.
• Syphilis may present with a single painless ulcer (chancre) in the genital area, but anal chancres can go unnoticed, hidden inside the rectum. Later-stage syphilis can cause rashes or systemic symptoms regardless of infection site.
• Shigella and Campylobacter, usually thought of as causes of foodborne illness, can be transmitted sexually through oral-anal contact. Symptoms can include diarrhea, abdominal pain, or fever. Unlike urogenital infections, these infections primarily affect the digestive tract and may be mistaken for “stomach bugs.”

The telltale signs of viral infections like herpes simplex virus type 2 (HSV-2) and human papillomavirus (HPV) can be overlooked if extragenital screening doesn’t occur, and anal sex increases the susceptibility of contracting HIV.

• HSV-2 can cause painful sores in the genital or anal area. Anal infections may be harder to spot and can mimic hemorrhoids or fissures, while genital HSV often produces more obvious blisters.
• HPV can cause warts or, over time, lead to anal cancer. Anal exposure increases risk for warts and precancerous lesions compared with genital-only exposure.
• HIV transmission is more efficient through anal intercourse than vaginal intercourse because the rectal mucosa is thinner and more prone to microtears.

These viral infections can’t be cured, but medications and vaccines help manage them and reduce the risk of complications. HIV can potentially be prevented using pre-exposure prophylaxis (PrEP) with daily oral medications. Post-exposure prophylaxis (PEP) is available for high-risk exposures after the fact, antiviral medications can reduce outbreaks and lower transmission risk of HSV-2, and HPV vaccination helps prevent anal cancer and genital warts.

Because many infections are mild or, at least initially, asymptomatic, individuals may unknowingly serve as reservoirs, harboring the infection, passing it along to others, and increasing the risk of HIV and other STIs.

A cornerstone of prevention is correct and consistent condom use. Condoms should be used every time, replaced after their expiration date, and never used with oil-based lubricants that can weaken the latex. Even though latex condoms are recommended, latex allergies can complicate matters – inflammation from an allergic reaction can damage the mucosal barrier and increase susceptibility to infection. It’s best to talk to your doctor about alternatives.

Open, nonjudgmental conversations between providers and patients are crucial for encouraging honest disclosure of sexual behaviors, past infections, and potential exposure risks. This information allows providers to offer site-specific testing, vaccinations, PrEP, and treatment if needed. Partner notification and empiric therapy (treating sexual partners even before test results come back) can reduce reinfection and transmission rates, curbing the spread of STIs within the community.

Additional Infection Risk

In addition to “classic” STIs, certain enteric pathogens (microorganisms that infect the GI tract and cause illness, generally through the fecal-oral route) are increasingly recognized in MSM and TNB populations. Shigella, E. coli, Campylobacter, hepatitis A virus (HAV), Giardia lamblia, and Entamoeba histolytica can all be transmitted through sexual activities involving oral-anal, digital (finger)-anal, oral-genital, and anal-genital contact.

Parasitic infections such as Giardia lamblia and Entamoeba histolytica burrow into cells in the gastrointestinal tract, sometimes leading to systemic illness. Bacteria such as Shigella or Campylobacter can lead to diarrhea, abdominal pain, or more severe complications.

Regular, site-specific testing is the best way to identify these hidden infections. By catching them early, individuals can get treatment, protect their own health, and reduce the risk of infection in their partners.

Myths and Misconceptions

Sexual health is an area where misinformation spreads easily and it’s often fueled by stigma, outdated beliefs, or incomplete understanding of how infections actually work. Accurate information not only supports safer practices but also helps reduce shame, encourages testing, and promotes respectful conversations about sexual wellbeing.

“Only LGBTQ+ people get anal STIs.”

Anyone who engages in anal receptive intercourse, regardless of sexual orientation, gender identity, or partner gender, can acquire anorectal STIs. The difference is not who someone is, but which sexual practices are part of their life and how often they’re screened.

“Anal STIs always cause symptoms, so I’d know if I had one.”

Up to 85% of rectal STIs are asymptomatic in MSM. Many people feel completely fine yet carry infections that can still spread or increase susceptibility to others, including HIV.

“If I don’t have anal sex, I can’t get infections in the rectum.”

Oral-anal contact, sex toys, digital (finger) penetration, and shared sexual devices can all introduce bacteria, viruses, or parasites into the rectum. Anatomy, not orientation, determines the risk.

“Hemorrhoids are the only reason for anal pain or bleeding.”

Anal discomfort, ulcers, discharge, or bleeding may also signal STIs like gonorrhea, chlamydia, syphilis, or HSV. These are symptoms of atypical health, could be something more serious than an STI, and warrant a trip to see your doctor.

“If my genital STI test is negative, I’m all clear.”

Urogenital testing (urine or genital swab) does not detect infections in the rectum or throat. Extragenital testing is essential for people who engage in anal or oral sex because infections commonly settle at the site of exposure.

“Condoms protect against everything during anal sex.”

Condoms are highly effective for many STIs, but infections spread through skin-to-skin contact, like HPV, HSV-2, or syphilis, can still be transmitted even when condoms are used correctly.

“Douching makes anal sex safer.”

While some people use enemas or douching for hygiene and preparation for anal sex, the overuse of these practices can irritate or damage the mucosal lining. A weakened mucosal barrier increases the risk of acquiring STIs.

“PrEP is only for people with multiple partners.”

PrEP (pre-exposure prophylaxis) is for anyone who wants a highly effective HIV prevention strategy – whether they have one partner or many, and regardless of sexual orientation or gender identity.

“Anal STIs aren’t a big deal – antibiotics fix everything.”

Some infections like gonorrhea and Shigella are becoming increasingly resistant to antibiotics, and chronic inflammation from untreated infections can raise the risk of HIV or cause long-term gastrointestinal symptoms.

“Talking openly about sexual practices is unnecessary or inappropriate.”

Honest, judgment-free conversations with healthcare providers allow for proper screening and treatment. Providers can only protect a patient’s health when they understand the full picture of their sexual practices.

If you’re experiencing rectal symptoms, have concerns about STI exposure, or simply want to stay proactive about your health, Dr. Schlussel and Dr. Crean provides comprehensive, judgment-free evaluation and testing – including colorectal symptom assessment and anal cytology for patients at higher risk of HPV-related disease. Don’t let apprehension over discussing sexual health get in the way. Call the team at MASJax Bariatric and General Surgery to schedule your appointment.

1. Tordoff, D. M., Dombrowski, J. C., Ramchandani, M. S., & Barbee, L. A. (2023). Trans-inclusive Sexual Health Questionnaire to Improve Human Immunodeficiency Virus/Sexually Transmitted Infection (STI) Care for Transgender Patients: Anatomic Site-Specific STI Prevalence and Screening. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 76(3), e736–e743. https://doi.org/10.1093/cid/ciac370.
2. CDC. (2021). Men who have sex with men (MSM). Www.cdc.gov. https://www.cdc.gov/std/treatment-guidelines/msm.htm. Sexually Transmitted Infections Treatment Guidelines, 2021.