Can You Take Antibiotics with Fertility Drugs? What the Science Says

October 10, 2025 •

4 min read

Interestingly, in certain fertility treatment cycles like IVF, reproductive specialists may actually prescribe antibiotics to help optimize conditions and prevent infection. The question of can you take antibiotics with fertility drugs? is complex and depends on the specific medication, dosage, and underlying medical context.

Quick Summary

It is generally safe to take necessary antibiotics with fertility drugs under a doctor's supervision. Some antibiotics can temporarily affect sperm quality, but the greater risk often lies with untreated infections. Communication with your healthcare team is essential.

Key Points

Doctor's Guidance is Essential: Always consult your fertility specialist before starting antibiotics while on fertility drugs to confirm the medication is safe and necessary.
Untreated Infection is a Greater Risk: An untreated bacterial infection can cause serious and permanent damage to reproductive organs in both men and women, making appropriate antibiotic treatment crucial.
Minimal Impact on Female Fertility: Most antibiotics do not directly affect female fertility, ovulation, or hormonal treatments; the risk from the infection itself is the primary concern.
Temporary Effect on Male Fertility: Some antibiotics can temporarily reduce sperm count or motility, but these effects are typically reversible within a few months after the treatment ends.
Infection Prevention in ART: In some IVF cycles, antibiotics like doxycycline may be prescribed to reduce the risk of infection and improve implantation conditions, though this practice is debated.
Microbiome Disruption is a Consideration: Antibiotics can alter the microbiome in the reproductive tract, which may have indirect effects on fertility, making informed medical decisions important.
Not All Antibiotics Interact: The myth that all antibiotics interfere with hormonal birth control is largely false, though a few specific types like rifamycins are exceptions.

The Complex Relationship Between Antibiotics and Fertility

The decision to take antibiotics while undergoing fertility treatment can be confusing, but it's important to understand the context. In some cases, clinics may even incorporate antibiotics into the treatment protocol itself. For instance, in an IVF cycle, doctors sometimes prescribe prophylactic antibiotics, such as doxycycline, to control bacteria that could potentially affect embryo implantation. This practice, however, is a subject of ongoing debate in the medical community. For individuals with a bacterial infection, antibiotic treatment is necessary. The key is to discuss any medications with your fertility specialist to ensure proper coordination and safety.

Impact on Female Fertility and Hormones

Research indicates that most antibiotics do not directly harm a woman's fertility or interfere with the hormones that regulate the menstrual and ovulation cycles. A necessary course of antibiotics is often less of a threat to fertility than the bacterial infection it's designed to treat.

Here are some key considerations for female fertility:

Untreated Infections: Conditions like chlamydia, pelvic inflammatory disease (PID), and chronic endometritis can cause significant and lasting damage to the reproductive tract, leading to blockages and scarring. In these cases, antibiotics are crucial for preserving fertility, not harming it.
Microbiome Disruption: Antibiotics can disrupt the delicate balance of the vaginal and gut microbiomes. While this disruption can lead to issues like yeast infections, the impact on fertility is less direct, though some research suggests microbiome health is related to IVF outcomes.
Specific Antibiotic Classes: Some studies have shown a weak association between certain antibiotic classes, such as macrolides and sulfonamides, and slightly reduced fecundability (the per-cycle probability of conception), but this link is not well understood and may be related to the infections being treated rather than the medication itself.

Effects on Male Fertility

For men, the impact of antibiotics is more direct but usually temporary. Certain antibiotics can affect sperm quality, including count, motility, and morphology. The good news is that sperm regenerates every 72 days, so any negative effects are not typically permanent.

Here's what to know about antibiotics and male fertility:

Sperm Quality: Antibiotics like tetracyclines, erythromycin, and nitrofurantoin have been shown to temporarily impair sperm function.
Reversible Effects: The effects on sperm quality typically resolve within a few months after the medication is discontinued, allowing for a return to pre-treatment levels.
Benefits of Treatment: As with women, treating an underlying infection can be beneficial for male fertility. Untreated infections, particularly sexually transmitted infections (STIs), can cause lasting damage to the reproductive system.
Consulting a Doctor: Men should inform their doctors about their fertility plans. A physician can prescribe an antibiotic that is less likely to affect sperm quality if an alternative is available.

Navigating Antibiotics During Assisted Reproductive Technology (ART)

During ART cycles like IVF and Frozen Embryo Transfer (FET), antibiotics may be used for specific reasons, but their efficacy is debated among specialists.

Typical antibiotic use during ART:

Prophylactic Administration: Some clinics prescribe antibiotics like doxycycline or a Z-pack during an IVF cycle, often starting around the time of egg retrieval, to prevent bacteria from interfering with implantation.
Treatment of Infection: If a patient has a known infection, whether it's chronic endometritis or another bacterial issue, antibiotics are used to treat it before or during the cycle to improve outcomes.

Debate on prophylactic use:

Some studies question the benefit of routine antibiotic prophylaxis before embryo transfer, noting that evidence to support its impact on pregnancy rates is weak. Concerns include the risk of antibiotic resistance and potential alteration of the reproductive tract microbiome. A 2021 review in Fertility and Sterility suggested that some prophylactic antibiotic use may be unwarranted and could potentially cause unintended negative effects.

Comparison: Effects of Antibiotics on Fertility


Aspect	Impact on Female Fertility	Impact on Male Fertility
Direct Hormonal Impact	Minimal to none; generally does not affect ovulation.	Minimal to none, though certain antifungals can affect hormones.
Sperm/Egg Quality	Low evidence of harm to egg quality; some classes weakly linked to lower fecundability.	Potential for temporary reduction in sperm count, motility, and morphology.
Reversibility	Effects are not typically an issue.	Effects on sperm are generally reversible within a few months after discontinuation.
Microbiome	Potential disruption of the vaginal and gut microbiomes, which could indirectly affect outcomes.	Potential disruption of the gut microbiome, though human data is limited.
Risks of Untreated Infection	High risk of permanent damage to reproductive organs, leading to infertility.	High risk of damage to sperm production and reproductive health.

What to Discuss with Your Doctor

Before taking any medication during fertility treatment, inform your healthcare team. It is essential to provide them with a complete list of all medications, including prescriptions, over-the-counter drugs, and supplements. This ensures they can check for potential interactions with your fertility drugs and choose the safest and most effective course of treatment. Your doctor can determine if an antibiotic is necessary, weigh its risks and benefits, and select one that is least likely to interfere with your treatment plan.

Conclusion: Medical Guidance is Key

The bottom line is that for most people, taking a necessary course of antibiotics under medical supervision is perfectly safe while on fertility drugs, and ignoring an infection presents a far greater threat to reproductive health. While some antibiotics may temporarily affect sperm quality, these effects are usually reversible. For women, the direct impact on hormones is minimal, and treating infections is often a vital step toward a successful pregnancy. The medical landscape surrounding prophylactic antibiotics in ART is still evolving, but for treating an active infection, there is little debate. Always communicate openly with your fertility specialist about any medications you are taking or planning to take to ensure the best possible outcome for your treatment. Research into the broader effects of antibiotics continues, so staying informed with reliable resources like the National Institutes of Health is a good practice.(https://pmc.ncbi.nlm.nih.gov/articles/PMC8581385/).

Frequently Asked Questions

Most antibiotics do not have a known interaction that reduces the effectiveness of fertility drugs. However, you should always inform your fertility specialist of any and all medications you are taking so they can assess your specific situation and treatment plan.

Some antibiotics, including tetracyclines, erythromycin, and nitrofurantoin, have been shown to temporarily and reversibly affect sperm quality. The effects typically resolve within a few months after stopping the medication.

Yes, many fertility clinics incorporate antibiotics into IVF protocols for infection prevention, particularly around the time of egg retrieval or embryo transfer. If you develop a bacterial infection during a cycle, your doctor will prescribe the safest and most effective antibiotic.

There is no strong evidence to suggest that standard antibiotics directly harm a woman's egg supply or interfere with the hormones that regulate ovulation. The greater risk to fertility often comes from untreated infections.

If you have an STI, it is critical to treat it with antibiotics. Untreated STIs like chlamydia can cause permanent damage to the reproductive organs, leading to conditions like PID that cause infertility. A short course of antibiotics to clear the infection is almost always the best course of action.

Yes, antibiotics can alter the bacterial balance of the vaginal microbiome. Some research suggests this imbalance could potentially affect IVF outcomes, though more investigation is needed. Doctors weigh this risk against the necessity of treating an infection.

For men taking certain antibiotics that affect sperm quality, doctors may advise waiting a few months after treatment is finished before a procedure like sperm freezing. For women, the decision depends on the infection being treated. In general, your doctor will provide the best guidance based on your specific health and treatment timeline.