Surviving SIBO Die Off Symptoms: What They Are & How to Prevent Them

Grace Clark-Hibbs

February 15, 2024

A common and simple way to explain SIBO die off symptoms is that, “it’s going to get worse before it gets better.” Which is basically saying that feeling worse after starting SIBO treatment is inevitable and means the treatment is working.

But it doesn’t have to be this way. In fact, we’re here to tell you that it IS possible to successfully get rid of SIBO without feeling even crappier than you already do.

But first…

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Note: This post was originally written in 2021 and has been updated in 2024.

What is SIBO?

SIBO or small intestinal bacterial overgrowth, is a condition defined as an imbalance of bacteria in the small intestine. This imbalance often leads to uncomfortable symptoms like bloating, gas, nausea, constipation, diarrhea, and sometimes nutrient deficiencies. (1, 2)

Correcting this imbalance involves a few steps:

  • Identifying and addressing what led to the SIBO in the first place (i.e. the root cause)
  • Rebalancing the gut – killing the “bad” bacteria and feeding the “good”
  • Preventing a relapse by healing the gut lining
  • Understanding how to troubleshoot and manage symptoms long term 

Unfortunately, even more uncomfortable symptoms can occur during the second step of treatment, which is sometimes referred to as the “kill” phase. These secondary symptoms are called die off symptoms.

This article will explain what die off is, why it makes you feel worse before you feel better, and actionable ways to reduce or prevent these uncomfortable symptoms.

Let’s dive in!

What is SIBO die off?

One theorized explanation is the Jarisch-Herxheimer reaction (JHR). The JHR was first discussed in the late 1800s when syphilis patients were observed to have worsening symptoms shortly after starting treatment. 

Today, the JHR is defined as a reaction that occurs within 24 hours of starting antibiotic treatment for certain infections including syphilis, Lyme disease, and relapsing fever. (3)

While this reaction was first discovered in syphilis patients, the reaction has now been observed in other bacterial, fungal, and protozoal (such as malaria and dysentery) infections. 

Moreover, it often goes undiagnosed because many of the most common symptoms are either present before treatment starts or get misidentified as an allergic reaction to the antibiotics. (3, 4)

Why do SIBO die off symptoms occur?

According to a recent review of the current research surrounding the JHR, the exact reason these symptoms occur is still unknown. (3)

That being said, the main theory suggests that when the bacteria, fungus, or whatever microorganism is causing the initial infection is dying off they will release toxins into the body, triggering an immune reaction. (5)

However, this theory is controversial and has little scientific evidence to support it at this time. 

How long do die off symptoms last?

In general, symptoms resolve on their own within 1-2 days of starting treatment, but everyone’s reaction to the JHR is different. (3)

The length of time the symptoms will last depends on a variety of factors, including: 

  • the severity of the infection 
  • the individual’s diet and lifestyle
  • what management/prevention strategies are being implemented

Lastly, more research involving die off specifically related to SIBO needs to be done in order to confidently connect the two. 

It’s also important to remember that worsening symptoms may simply be because the bacterial overgrowth is not being treated correctly. (7)

This is one more reason why it’s so important to work with an experienced medical professional during treatment. 

What are the symptoms of SIBO die off?

The most common symptoms include: (3, 4, 5, 6)

  • Low grade fever
  • Chills
  • Skin rash
  • Body aches
  • Headaches
  • Low energy/Fatigue
  • Hyperventilation
  • Gas, bloating, diarrhea and/or constipation
  • Sleep issues

Other, less common but more severe symptoms include: (5)

  • Meningitis
  • Respiratory failure
  • Liver and kidney disfunction
  • Heart issues
  • Early uterine contractions in pregnant women
  • Increased risk for strokes and seizures

Although these less common symptoms sound serious and a little scary, there is little to no evidence the JHR is fatal or long lasting. (5)

How do you distinguish die off symptoms from other SIBO symptoms?

Things like bloating, gas, diarrhea and/or constipation can all show up during the initial SIBO infection and can worsen during the initial phase of treatment. Other symptoms that have been shown to overlap include neurological symptoms like headaches and fatigue

You can distinguish between the two by assessing when the symptoms started or got worse and how long they lasted. Die off symptoms will come on within a few hours of start of treatment and should resolve or lessen in intensity within a few days.

Can die off be treated/prevented?

The primary method of treatment is symptom management. This includes over-the-counter drugs to treat fever, body aches, and headaches (i.e. Tylenol or ibuprofen) and antihistamines to help with skin rashes and itching. (3, 5)

Other recommendations include:

  • Eating enough and a variety of dietary fiber – This keeps your bowels moving and allows your kidneys and liver to effectively do their jobs. (8)
  • Drink lots of fluids – This helps to flush out toxins produced while treating SIBO through the urine.
  • Stress management – High levels of stress impairs your immune system and makes it harder to recover from illness or injury. It also depletes your mineral stores faster, which are essential for almost every process in the body. Be intentional about what relaxes you and incorporate that into your daily routine.
  • Prioritize sleep – A lot of detox happens while you’re asleep. Aim to consistently be in bed by 10PM and to get 7-9 hours of sleep each night.
  • Limit alcohol – It’s best to avoid all alcohol during the SIBO treatment process. If that’s not realistic for you, limit alcohol intake to no more than 2 drinks per week
  • Support the body’s natural detox pathways (i.e. lymphatic system, liver, kidneys) – Some ways to do that include:
    • Head to the infrared sauna 3x per week for 10-20 minutes each time
    • Use a castor oil pack at least 4 days per week for at least 2 hours at a time
    • Drink 1 cup of milk thistle tea per day
infographic the explains the six tips for preventing SIBO die off symptoms

If symptoms don’t resolve in a couple of days and/or get worse, talk to your healthcare provider immediately. If symptoms become severe (i.e. trouble breathing, rash that covers a large portion of the body, high fever that doesn’t go away), go to the hospital.

Final Thoughts

Die off symptoms are believed to be caused by a phenomenon called the Jarisch-Herxheimer reaction, which was first observed in syphilis patients. It is now believed to occur during the treatment of other infections, including SIBO. 

Die off symptoms will not affect everyone, but they can be very uncomfortable for those that they do affect. Focusing on supporting the body’s natural detox pathways, drinking plenty of fluids, and getting enough sleep are the best ways to prevent these symptoms from occurring.

If you do end up experiencing die off symptoms, they should resolve on their own within a day or two, however if they are not resolving or are getting worse, see your health care professional or go to the hospital immediately.

If you’ve been struggling with SIBO, bloat, constipation or other IBS symptoms and need some insight into your root causes, check out my Why Am I STILL Bloated Quiz!

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Remember: this post is for informational purposes only and may not be the best fit for you and your personal situation. It shall not be construed as medical advice. The information and education provided here is not intended or implied to supplement or replace professional medical treatment, advice, and/or diagnosis. Always check with your own physician or medical professional before trying or implementing any information read here.

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Grace sitting

Hi, I’m Grace!

A registered dietitian & gut health expert based in Portland, OR with my husband & orange tabby, Tony.


And I’ve been in your shoes!


As someone who has struggled with my own severe, chronic, & painful bloat & constipation for over 15 years, I understand what it’s like not to get answers from conventional medical support.


This is why I’ve made it my mission to help everyone who feels held back & defeated by their gut find freedom from their embarrassing symptoms FOR GOOD!

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Why am i STILL bloated?!?


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