Can Hidden Infections Affect Fertility? Understanding NAAT Testing

Certain infections may affect your ability to conceive without causing noticeable symptoms. But if left untreated, they can harm your reproductive health. Our experts explain how certain diagnostic tests, like nucleic acid amplification tests (NAATs), can help detect these infections with high accuracy.

Pregatips
Many factors may lead to failure in conception even after trying. Your doctor may recommend various medical investigations to identify the reasons why you may be experiencing difficulties getting pregnant. In some cases, the issue may not be apparent right away.
Some of the most common STIs, including chlamydia and gonorrhoea, might be the reason. These infections might be affecting your reproductive health silently for a long time without showing any symptoms.

In fact, such infections might be causing damage to your reproductive organs if not diagnosed and treated on time.

To accurately diagnose these infections, your doctor may recommend a nucleic acid amplification test (NAAT).

Knowing about this test may help you get an early diagnosis and reduce the risk of fertility-related complications.

What Is A NAAT Test?

NAAT stands for nucleic acid amplification test. This medical test is based on identifying the genetic material (DNA or RNA) of bacteria or viruses rather than waiting for them to grow in a laboratory. Moreover, it can detect infections even when the causative agents are present in an undetectable count.

The following are the common infections for which NAAT is indicated:

Kind of Infection
Consequences If Left Untreated
Chlamydia
May damage the fallopian tubes
Gonorrhoea
May increase the risk of pelvic inflammatory disease (PID)
Trichomoniasis

(such testing parameters may vary among laboratories)
May lead to inflammation in the reproductive tract

How Can Undiagnosed Infections Affect Your Fertility?

Some infections cause little or no discomfort. However, they may slowly spread through the reproductive tract.

This can lead to:

However, not everyone with these infections develops fertility problems. If the infection is present, early diagnosis lowers the chance of long-term complications.

When May Your Doctor Recommend This Test?

Your doctor may advise this test if you have:

  • Difficulty conceiving
  • A partner diagnosed with an STI
  • Abnormal discharge from the vagina or penis
  • Painful urination
  • Unexplained pelvic pain
  • Vaginal bleeding after sexual intercourse
  • Multiple sexual partners
  • A positive history of untreated STIs
In fact, this testing may be advised as a screening test before fertility treatment.

What Are The Sample Collection Methods?

The sample collection is usually quick.

Depending on the infection being tested, your healthcare provider may collect:

Type of Sample
Important points
Urine sample
First-catch urine
Vaginal swab
Collected by a healthcare professional or self-collected in selected settings
Cervical swab
During a pelvic examination
Urethral swab
When clinically required
Most people can return to their normal routine immediately after the test.

What Do NAAT Results Indicate?

The laboratory usually reports the result as positive or negative.

Result
Inference
Treatment Plan
Positive
Infection detected
Your doctor will discuss appropriate treatment and partner management if required
Negative
Infection not detected
Further fertility tests may be needed if symptoms or infertility continue.
Your doctor will interpret the result along with your symptoms, examination findings, and medical history.

How Can NAAT Testing Help You?

Treating an infection prevents further damage to your reproductive organs.

However, treatment cannot always reverse scarring that has already developed.

Therefore, early testing is important.

If an infection is diagnosed:

  • Complete the prescribed treatment.
  • Follow your doctor's advice about follow-up testing.
  • Your sexual partner may also need testing and treatment.
  • Avoid sexual contact until your healthcare provider confirms it is safe.
Prompt care helps protect both your reproductive health and future fertility.

How Can You Reduce The Risk Of Fertility-Related Infections?

Simple preventive steps can make a difference.

  • Practise safer sex by using condoms correctly.
  • Attend regular sexual health check-ups if you are at increased risk.
  • Do not ignore unusual discharge or pelvic pain.
  • Get tested if your partner has been diagnosed with an STI.
  • Complete treatment exactly as advised.
  • Discuss STI screening before planning a pregnancy, especially if you have risk factors.
Your doctor may recommend NAAT tests to investigate the cause of your infertility early. This can enable you to receive timely care.

You’re not alone in your journey when trying to conceive. Join our supportive community to connect with others, share experiences, and find encouragement every step of the way.

FAQs on Can Hidden Infections Affect Fertility? Understanding NAAT Testing

  1. Can I have chlamydia without any symptoms?
    Yes. Many people with chlamydia have no symptoms. Therefore, testing is often the only way to detect the infection early.
  2. Is a NAAT test painful?
    Usually not. A urine sample causes no discomfort. Swab collection may feel slightly uncomfortable, but it is generally brief.
  3. Is the NAAT test always necessary before trying to conceive?
    It is not a routinely recommended test for everyone planning a pregnancy. Your doctor may recommend it based on your history and symptoms.
Medically Reviewed By:
Dr Kanchi Khurana, Associate Director - Department of Fertility, Cloudnine Group of Hospitals, Chandigarh
How we reviewed this article
Our team continuously monitors the health and wellness space to create relevant content for you. Every article is reviewed by medical experts to ensure accuracy.
  • Current version
  • Aug 19, 2026, 11:34 AMReviewed by
  • Aug 19, 2026, 11:34 AMWritten byDr. Kanika Sharma