An STI in the anus needs a different sample than a standard STI test. Gonorrhoea and chlamydia in the rectum are only found with a swab of the anus; syphilis and HIV need blood; herpes needs a swab of a blister. One test does not cover this.
That sounds more awkward than it is. You only need to know which sample belongs to which risk, and that is exactly what this page covers.
We start with the infections themselves, then the practical side of taking the sample.
Which STIs can you get in your anus?
The STIs that can sit in the anus or rectum are gonorrhoea, chlamydia, LGV, syphilis, herpes and HPV. The European guideline names gonorrhoea, chlamydia including LGV, syphilis and herpes as the most common pathogens in that spot (de Vries, 2021). HPV sits there too, but behaves differently: you see it as warts.
They differ sharply in how loud they are.
| STI | Symptoms in the anus | Which sample | In our CGT test |
|---|---|---|---|
| Chlamydia | Usually none | Anal swab (PCR) | Yes, with an anal swab |
| Gonorrhoea | Often none, sometimes mucus or pain | Anal swab (PCR) | Yes, with an anal swab |
| LGV | Sometimes heavy, sometimes none | Anal swab plus typing | Partly, typing is extra |
| Syphilis | Painless sore | Blood test | No, separate test |
| Herpes | Painful blisters | Swab of a blister | No, separate test |
| HPV | Warts, usually painless | Visible on examination | No, no standard test |
The top two rows matter most, because those two are the most common and give away the least. For HPV around the anus, warts around the anus is the separate piece.
How do you notice an STI in your anus?
Usually you do not. The European guideline states that the majority of rectal chlamydia and gonococcal infections run without symptoms (de Vries, 2021), and a study on Reunion island found that every extragenital infection it detected was symptom-free (Calas, 2021).
When there is something, it is mucus or pus, itching, pain, an empty urge, or some blood. That combination is called proctitis, and we work it out in proctitis: symptoms, causes and testing.
The trouble is that those symptoms resemble ten other things.
Haemorrhoids, a fissure, an irritable bowel. Without the context of what happened in the preceding weeks, the symptom points you nowhere. The same holds more broadly for STIs without symptoms.
How does an anal STI test work?
With a cotton swab that goes a short way into the anal canal and is rotated. The lab examines that swab with a PCR, the same technique your GP and the public health service use. A result is usually back within a few working days.
It is not an internal examination. The swab goes in about two to three centimetres, and that is all.
Our test for chlamydia, gonorrhoea and trichomonas runs on that PCR. Choose an anal swab when ordering if that is where your risk sat; the standard sample looks at the genital side.
Can you take an anal swab yourself?
Yes, and the result is just as good. In a 2024 study, throat and rectal swabs taken at home were no less reliable than swabs taken in a healthcare setting (Orser, 2024).
For a lot of people that is the point where testing suddenly becomes doable.
The barrier with an anal test is rarely the needle or the lab. It is the conversation you would have to have to get one. That is precisely why testing at home exists.
When is the best time to test after a risk?
For chlamydia and gonorrhoea, about two weeks after contact is a common moment; for syphilis and HIV it takes longer before a blood test is reliable. Testing too early gives you a result that rules nothing out.
The full timeline per STI is in how long after unprotected sex you can test.
If you have symptoms that are not going away, do not sit out that window. With symptoms a doctor can look sooner and sometimes see something already.
Does a condom protect against an anal STI?
It clearly lowers the risk, but it rules nothing out. The European guideline puts it bluntly: condom use does not guarantee protection from STIs, which are often spread without penile penetration (de Vries, 2021).
Fingers, toys and skin-to-skin contact all count. That makes "was there a condom" a poorer measure of risk than people assume.
The useful question is: was there receptive anal contact.
Picture two men who both use condoms consistently and get tested every 3 months.
One submits urine only, the other adds an anal swab. The second turned up something that could have stayed unnoticed in the first for months. I think that is the strongest argument against "but I already test".
The RIVM tracks Dutch STI figures through the sexual health centres, where anal infections are included as standard for certain groups. That is not for nothing: it is the spot a normal test looks past. If you test regularly, see also STI testing for MSM.
References
- de Vries HJC, et al. 2021 European Guideline on the management of proctitis, proctocolitis and enteritis caused by sexually transmissible pathogens. Journal of the European Academy of Dermatology and Venereology, 2021. PMID 34057249.
- Calas A, et al. Prevalence of urogenital, anal, and pharyngeal infections with Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium: a cross-sectional study in Reunion island. BMC Infectious Diseases, 2021. PMID 33478403.
- Orser L, et al. Testing for extragenital Neisseria gonorrhoeae and Chlamydia trachomatis: At-home pharyngeal and rectal self-swabs are non-inferior to those completed in healthcare settings. PLoS One, 2024. PMID 38768150.
- Chan PA, et al. Extragenital Infections Caused by Chlamydia trachomatis and Neisseria gonorrhoeae: A Review of the Literature. Infectious Diseases in Obstetrics and Gynecology, 2016. PMID 27366021.
- RIVM, STI surveillance Netherlands. Accessed August 2026.
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Discreettest
Dr. Naimi, BIG-registered physician, oversees the medical standards behind our content and assessments. Read our medical policy
