Every parent wants to keep their baby healthy, especially in the first year, when colds and viruses seem to pop up constantly. While it’s impossible to prevent every sniffle, there are proven ways to strengthen your baby’s immune system from the very beginning.

Immune health has been a major focus amongst clinicians and the general public since the COVID-19 pandemic. The importance has not excluded the pediatric population, especially the most vulnerable: infants. Whether COVID or another common virus, parents are increasingly seeking ways to prevent, treat, and enhance the function of the immune system both now and in the future.

From pregnancy to the first year of life, many factors shape how an infant’s immune system develops, including maternal nutrition, breastfeeding, gut health, stress, and everyday care. In this article, Dr. Tim Benik, pediatrician and Bébé Foodie advisor, shares his advice on what really supports infant immune health, what’s normal when it comes to infections, and when to check in with your pediatrician.

How your baby’s immune system develops before and after birth

Your baby’s immune system starts forming well before birth. Both maternal and paternal health play a role, influencing how strong a baby’s defenses are in the prenatal and neonatal period.

Let's look at some of the ways parents can shape that early immunity, from how your diet influences your baby’s health to how babies actually “borrow” protection from you in the first months

Have you heard of epigenetics? Here’s how your diet shapes your baby’s health

Epigenomics (changes in gene expression based on environmental factors, such as nutrition) may have a crucial importance for a fetus that can last well into adult years. The epigenetic changes that occur secondary to nutrition, for example, (whether “poor” or “excellent” nutritional status), can alter the reproductive health of the father and mother, which in turn has implications for the immune system of the fetus.

Bébé Foodie advice: Think of everyday swaps:

• Add salmon or chia seeds → omega-3s.

• Spinach or lentils → folate and iron.

• Nuts or seeds → zinc.

These simple choices during pregnancy can “teach” your baby’s immune system to function at its best.

Maternal transfer of immunity: Or how your baby "borrows" your immunity in the early months

Babies’ immune systems rely heavily on maternal transfer of immune factors, in particular immunoglobulins, via the placenta in utero and human milk postnatally. Infants begin to produce immunoglobulins on their own at a higher rate after 6 months of age, making maternal immunity especially important early on.

Bébé Foodie advice: If possible, continue breastfeeding in the early months. Even partial breastfeeding gives babies access to protective antibodies. If formula feeding, choose an iron-fortified option and discuss with your pediatrician about formulas that include added DHA.

How does breastfeeding support infant immune health?

Breastmilk does more than nourish, it actively delivers immune protection. It contains antibodies (especially secretory IgA) that coat the baby’s gut lining and help block viruses and bacteria from entering the bloodstream. It also provides white blood cells and other immune factors that act as a first line of defense, particularly in those early months before a baby is making enough of their own.

When mothers maintain good nutrition (or supplement if needed with vitamin D or omega-3s), their milk can pass along these nutrients, further supporting their baby’s developing immune system. It’s one of those small, everyday ways that nourishing yourself also nourishes your baby’s defenses.

But if breastfeeding isn’t your path, your baby can still thrive. Formula is carefully designed to meet your baby’s nutritional needs, including immune-supporting vitamins and minerals. What matters most is that your baby is fed, loved, and cared for in a safe environment.

Breastfeeding benefits include:

• Antibodies (especially secretory IgA) that coat the baby’s gut lining
  

• White blood cells and immune factors as a first line of defense
  

• Transfer of nutrients like vitamin D and omega-3s when maternal intake is adequate
  

• Adaptability over time (colostrum vs. mature milk) to meet changing needs

Bébé Foodie advice: If you’re breastfeeding, support your own nutrition with foods rich in vitamin D (eggs, fortified milk), omega-3s (salmon, chia seeds), and probiotics (yogurt, kefir). If you’re formula feeding, know that modern formulas are fortified with key nutrients, and your pediatrician can guide you if your baby needs additional supplementation. Both paths support your baby’s growing immune system.

👉 Wondering how much milk your baby really needs, whether breastmilk or formula? Check out our full guide to milk quantity here.

Your baby’s gut and immunity: why the microbiome matters

One of the key ways babies build their immune systems is through the evolution of the microbiome, specifically the gut flora. The biodiversity of the gut flora begins in utero and is impacted in a positive way from:

• Vaginal delivery
  

• Early and continued breastfeeding
  

• Avoiding antibiotics unless absolutely necessary
  

• Using targeted probiotics (such as lactobacillus reuteri and bifidobacterium infantis) when appropriate

Bébé Foodie tip: If your baby was born by C-section or needed antibiotics early on, talk with your pediatrician about probiotics designed for infants. Even simple food exposures later, like plain yogurt or kefir when solids begin, can help introduce good bacteria.

Vaccines, colds, and daycare germs: why exposure can actually help

It’s impossible (and not healthy) to keep your baby in a germ-free bubble. In fact, the most direct stimulation of an infant’s evolving and strengthening immune system is exposure to a virus, whether via vaccination or contraction of the virus itself.

The latter, often causing angst amongst parents, has profound benefits for the developing microbiome, and there is literature showing the benefits of early pathogen exposure, which is one reason parents are discouraged from pulling their child out of daycare due to frequent infections, except in unique cases (significant underlying chronic disease).

Bébé Foodie tip: Stay on track with your baby’s vaccination schedule, and don’t panic about daycare germs. Think of every runny nose as your baby’s immune system training for the future.

Stress and infant immune health

As babies grow and develop through infancy, there are other environmental and behavioral modifications that significantly impact the function of their immune system.

Why chronic stress can weaken a baby’s immune system

One of the most overlooked aspects of infant health, and in this case, infant immune health, is stress. While acute stress can be beneficial (crying at the first indication of hunger or pain), chronic stress is pro-inflammatory. Chronic stress has many negative implications for the fragile immune system of an infant. It releases unhealthy levels of pro-inflammatory cells, such as cytokines. It also impairs T-cell regulation, which has importance in immune homeostasis and the prevention of autoimmune disease.

Everyday causes of stress in infants (and what parents can adjust)

These processes are often secondary to changes in the gut microbiome, which has direct signaling from the nervous system. Important factors contributing to infant chronic stress include:

• Poor nutrition (including maternal nutrition via breastmilk)
  

• Lack of bonding (parental depression and anxiety, for example)
  

• Poor or disrupted sleep
  

• Air pollutants, such as cigarette smoke
  
  

Bébé Foodie tip: Focus on simple calming routines. Regular naps, skin-to-skin cuddles, and a smoke-free home can do wonders for reducing stress signals in your baby’s body.

Nutrition, vitamins, and immune support in the first year

Whether via breastmilk or direct feeding (around 6 months of age and beyond), specific nutrients begin to take on more importance for an infant’s ability to respond appropriately to the number of pathogens they come into contact with in their first year, many of which are viruses that cause upper respiratory symptoms.

How the gut supports nutrient absorption for immunity

As detailed above, the gut microbiome plays a key role in maintaining a strong immune system. In addition to preventing chronic stress, another important aspect of building a diverse gut flora is to strengthen the gut’s mucosal barrier. 

The gut isn’t just for digestion, it’s home to most of the immune system. A healthy gut lining acts like a protective gatekeeper: it absorbs vitamins, minerals, and fats babies need for growth, while keeping out harmful bacteria or toxins. When the mucosal barrier is strong, nutrients such as vitamin A, vitamin D, zinc, and omega-3 fatty acids can be absorbed more effectively, directly fueling the immune cells that line the gut and circulate throughout the body.

Gut bacteria also “train” the immune system, teaching it to recognize what’s safe (like food proteins) and what might be harmful (like viruses). This early education helps reduce unnecessary inflammation and may lower the risk of allergies or autoimmune problems later on.

Key nutrients for supporting infant immune health

Fat-soluble vitamins such as vitamin A and D, and omega-3 fatty acids (EPA and DHA), play a crucial role in maintaining the integrity of the mucosal barrier via strengthening of tight junctions and the cell membrane, respectively.

It is important to note that the fat content of both breastmilk and formula will meet the nutritional demand of an infant through the first year of life, assuming they are consuming roughly 25-30 ounces per day.

Vitamin A deficiency is rare in the developed world, and the majority of breastfeeding mothers will have adequate levels in their breastmilk.

Vitamin D and omega-3s: why they matter for babies

Vitamin D and omega-3 fatty acids are frequently not at desirable levels in many adults, and this has a direct negative correlation with breastmilk levels. This is why for breastfeeding infants, the recommendation is daily supplementation of 400 international units.

For omega-3 fatty acids, there is more of a grey zone in terms of intake. Most recommendations focus on infants getting 500 mg total daily, with breastfeeding mothers consuming a minimum of 200-300 mg of DHA daily.

While the importance of DHA has been widely tied to the neurodevelopment of the infant, there are significant immune-boosting properties that both DHA and EPA provide.

Bébé Foodie tip: When starting solids around 6 months, offer foods like mashed salmon (DHA), puréed sweet potato (vitamin A), or lentils (iron + zinc). Small bites of these “immune foods” are a great way to build strong defenses naturally.

Baby colds and infections: what’s normal and when to call your pediatrician

Even with the best routines, your baby will get sick — and that’s okay. Most babies catch 8–10 colds in their first year. Fevers, runny noses, and coughs are a sign the immune system is working, not failing.

When to call your pediatrician:

• Fever lasting more than 7 days.

• Trouble breathing (labored, fast, or chest retractions).

• Severe lethargy or unusual sleepiness.

• Unusually frequent or severe symptoms.

Signs your baby’s immune system may need extra support

Concerning symptoms that would signify the immune system is having a difficult time dealing with a pathogen include:

• Prolonged fever lasting more than 7 days
  

• Respiratory retractions or labored breathing
  

• Severe or unusual lethargy
  

• Frequent severe symptoms with each illness
  

• Lab results showing unexpected bacterial growth linked to suppressed immunity

Everyday ways to help your baby’s immune system thrive

Parents are encouraged to take a positive approach to keeping their baby safe and healthy from an immunity standpoint. While stressful early on, parents should explore ways to keep their health and their baby’s health optimized through robust nutrition and a safe, loving home environment. These first months of the baby’s life can have a large positive effect throughout the lifespan.

Don’t chase perfection, focus on consistency. Every cuddle, balanced meal, and good night’s sleep adds up to a stronger immune system for your baby!

References:

Pediatric Nutrition 8th ed. Chapter 35: “Nutrition and Immunity” 2020.

Integrative Medicine 5th ed. Chapter 33: “Integrative Medicine and Immune Support” Alschuler and Shroff. 2023.

American Society for Microbiology. “Baby immune systems aren’t immature, they’re just different” Barron. 2024.

 

Written by Dr. Tim Benik, DO

Pediatrician & Advisor at Bébé Foodie

Dr. Timothy Benik is a board-certified pediatrician at Cleveland Clinic with a background in both general pediatrics and integrative medicine. A fellow of the American Academy of Pediatrics, Dr. Benik brings a thoughtful, evidence-based approach to child nutrition. At Bébé Foodie, he serves as a trusted advisor, helping parents navigate safe and enjoyable feeding practices. He’s passionate about making the food journey a positive experience for both kids and caregivers.

This blog post is for information purposes only and shouldn’t be used as personal, health, nutritional, or medical advice. Always consult with your pediatrician before making any decisions about your child's health or readiness for various foods.