Food is a cornerstone of health, and the healthier your choices are, the healthier you’ll be. However, the modern Western diet, which is filled with ultraprocessed food, is anything but healthy. These products are made with synthetic ingredients that ultimately drive chronic disease.
Now, a new study goes into the mechanisms of ultraprocessed foods, and the findings are shocking. Researchers found that these products reshape your body at the genetic level by rewriting biological instructions, silencing protective genes and activating harmful ones, and basically creating cellular chaos.1
Ultraprocessed Foods Leave Chemical Marks on Women’s DNA
In a pilot study published in Nutrients, researchers from the University of São Paulo in Brazil investigated how diets high in ultraprocessed foods affect chemical markers on deoxyribonucleic acid (DNA) — also known as DNA methylation — among adult women. Specifically, the team wanted to know whether people who eat more of these highly refined foods show measurable differences in gene regulation compared to those who eat less.2
To test the hypothesis, the team analyzed the blood of 30 women divided into two groups — those who ate 14% of their daily calories from ultraprocessed foods and those whose daily calories were 45% ultraprocessed foods. From there, each participant’s DNA was examined using sequencing technology.
• The team found striking results — After analysis, 80 regions of the genome had clear differences in methylation between the high- and low-intake groups. Most of these differences showed hypomethylation in the women consuming the most ultraprocessed foods.
Basically, hypomethylation means that the molecular “off” switches that keep genes quiet were less active, leaving those genes more open to being turned on. When this pattern shows up in metabolic and inflammatory genes, it can lead to disruptions in how your body processes energy and controls inflammation.
• Damage builds up through the years — The women in the study were between 26 and 36 years old, with an average body mass index (BMI) of 24.7. No significant differences in total body fat, waist size, or blood sugar were noted between groups. In other words, DNA changes occurred even before traditional signs and symptoms of metabolic problems showed up.
• Examining genes affected by ultraprocessed food — When the researchers compared gene regions most affected, several stood out, including REPIN1-AS1 and FOXP1-AS1. These two are both linked to fat storage, insulin sensitivity, and cancer progression. REPIN1, for instance, helps regulate how your body stores fat and uses glucose — when its methylation pattern changes, it can alter how efficiently you burn or store energy.
FOXP1, another gene affected, plays a role in immune and brain function. In fact, the authors emphasized that it “has been linked to autism and hematologic cancers.”3
• A healthier diet leads to better methylation — The study noted that women who ate fewer ultraprocessed foods naturally consumed more protein and healthy fats — both essential for methylation balance. Nutrients that help this process include folate, vitamin B, choline, and docosahexaenoic acid (DHA).
The takeaway here is clear — eating large amounts of packaged snacks, frozen meals, sugary drinks, or processed meats send chemical messages to your genes, altering the way they perform. Thus, it’s in your best interest to minimize your intake of ultraprocessed foods to helps your genes function the way nature intended — maintaining balance, energy, and repair.
Childhood Diets Leave Lasting Marks on DNA Function
Children are also experiencing altered DNA methylation. In a large-scale analysis published in Clinical Epigenetics, researchers examined whether children who eat more ultraprocessed foods show measurable changes in their DNA methylation patterns.4
This team selected 3,152 children aged 5 to 11 years across four major European cohorts — Human Early-Life Exposome (HELIX), Generation XXI, Avon Longitudinal Study of Parents and Children (ALSPAC), and Generation R. Daily diets were recorded, from breakfast cereals and packaged snacks to sweetened drinks and fast-food meals, then blood samples were analyzed using high-resolution genetic arrays.
• How eating more ultraprocessed foods changed methylation in ways that alter biological function — Even after adjusting for variables like age, sex, body weight, parental education, and screen time, the results were clear — children consuming higher proportions of ultraprocessed foods had DNA methylation differences at seven specific genetic locations, called CpG sites.
Although the differences weren’t large enough to meet the most stringent thresholds for genome-wide significance, they were consistent across cohorts and tied to known biological systems, particularly thyroid hormone and liver function.
• Consumption of ultraprocessed food is widespread among children — When the researchers examined dietary records, they found wide differences between countries. In the U.K. cohort, ultraprocessed foods made up 57% of daily energy intake, while in America, that figure goes up to 66%.
Conversely, children in other countries generally ate lower amounts of ultraprocessed food, such as Colombia (19%) and Romania (15%). Yet even at these lower levels, DNA methylation differences still appeared.
• Effect of impaired methylation on children’s health — One of the strongest findings involved the ATF7 gene, which was more methylated in children with higher ultraprocessed food intake. ATF7 helps control stress-response signaling and influences how the body manages fat cells and inflammation.
Higher methylation of the said gene has been associated in other research with neurodevelopmental issues in children and metabolic imbalance in adults. In plain terms, eating more processed foods seems to put stress on the genes that help regulate metabolism and immune balance.
• Another key region affected was near the NHEJ1 gene — This region is involved in DNA repair, and when methylation increases here, it can interfere with how effectively your cells fix genetic damage.
• The study also found lower methylation near the PHYHIP gene — Among pregnant women, lower methylation at the mentioned site has been observed to affect visual health of children during growth.5
• How ultraprocessed food affects children’s health — The study provided insight into how ultraprocessed food ultimately affects thyroid health, which controls growth, energy, and metabolism:6
“[S]tudies have reported that some food additives are related to thyroid hormone dysregulation and an increased risk of subclinical thyroid dysfunction. A recent report on the HELIX data showed that metabolites associated with UPF intake were associated with C-peptide levels in children, a well-known marker of β-cell function and insulin resistance.
However, a wide range of non-methylation mechanisms that include the gut microbiome, oxidative stress, and inflammation are likely to be more affected by UPF intake and by the contaminants (acrylamide, etc.) and additives (emulsifiers, sweeteners, etc.) that they contain.”
For parents, these findings are an eye-opener. The study shows that every meal and snack choice sends a signal to your child’s cells that either reinforce healthy gene control or introduce harmful patterns. Hence, choose healthy, whole foods as much as possible, not ultraprocessed ones.
Break Free from the Clutches of Ultraprocessed Food
Companies have done extensive research into making ultraprocessed food a hit for consumers. They’re designed to be tasty and convenient, which appeals to modern, busy lifestyles. Moreover, they light up the reward circuits in your brain, making you crave them all the time. In short, they’re made to be addictive.
However, as the research shows, eating ultraprocessed foods won’t do any good for your DNA methylation, or other systems for that matter. In a previous article, I noted that ultraprocessed food increases the risk for a multitude of diseases — 32 of them, to be exact. That said, here are my recommendations to help you break the cycle for you and your child:
1. Revamp your pantry — Begin by changing what you stock at home because what you keep on hand shapes your family’s eating habits. Replace fast-grab snacks like chips, cookies, and processed bars with healthier choices that truly nourish you — fresh fruit, pastured eggs, homemade, grass fed yogurt. When junk food isn’t in sight, it’s far easier to make healthier choices.
2. Add protein and fiber to every meal — These two components help stabilize blood sugar levels and improve satiety, preventing you from eating too much (as well as keeping you away from junk food). Include quality proteins like pastured eggs, grass fed beef, or wild-caught salmon, and pair them with fibrous foods like vegetables, fruit, or whole grains.
3. Choose healthier versions of foods you enjoy — You don’t need to give up your favorite textures or flavors, just upgrade them. For example, swap sweetened yogurt for plain yogurt with fresh fruit, chips for air-popped popcorn, and soda for sparkling water with lemon or lime. You’ll still enjoy the crunch or fizz you crave but without the synthetic additives and vegetable oils that wreck your health.
4. Redesign your kitchen with a focus on health — Keep the healthiest foods within easy reach and the temptations out of sight. Move fresh fruit to eye level, store cut vegetables in clear containers, and stash processed snacks where you won’t see them often. Your brain responds to visual cues — when whole foods are visible, you’re far more likely to eat them.
5. Read ingredient lists carefully — You don’t need to memorize every chemical or ingredient — just scan for patterns that stand out. For example, long ingredient lists often signal heavy processing. Avoid refined sugars and vegetable oils such as soybean, corn, or sunflower oil. A shorter ingredient list typically means fewer industrial formulations and more real food.
6. Plan your treats properly — Instead of cutting out your favorite foods completely, schedule them intentionally. Pick one meal or event each week to enjoy something special, fully and without guilt. When you plan these moments, you remove the emotional baggage that often drives binge eating and regain a sense of control over your food choices.
7. Build a support network — Changing habits is easier when others understand your goals. Share your intentions with friends or family or join a community focused on whole-food eating. If you want a personalized plan, work with a registered dietitian nutritionist (RDN) who can align strategies with your specific health goals and make your progress sustainable.
Frequently Asked Questions (FAQs) About How Ultraprocessed Foods Affect DNA Methylation
Q: What did researchers discover about how ultraprocessed foods affect your DNA?
A: Scientists from the University of São Paulo found that eating large amounts of ultraprocessed foods changes how your genes behave. In their study, women whose diets were 45% ultraprocessed had 80 regions of their DNA chemically altered. These changes disrupted how their bodies control inflammation, metabolism, and fat storage. Even without visible signs of illness, like high blood sugar or excess body fat, their DNA was already showing damage.
Q: How early in life do these effects begin?
A: According to a study published in Clinical Epigenetics, the same kind of DNA alterations appear in children. Researchers analyzed 3,152 kids (aged 5 to 11) and found that those who ate more ultraprocessed foods had measurable changes in genes tied to thyroid function, liver health, and brain development. These effects appeared regardless of body weight, meaning the biological damage starts well before any outward symptoms of disease.
Q: What do these DNA changes mean for your health?
A: The studies revealed that ultraprocessed foods interfere with DNA methylation, which is a process that helps switch genes on and off. When this process falters, protective genes are silenced and harmful ones become more active. Over time, this weakens your ability to regulate blood sugar, control inflammation, repair damaged cells, and maintain hormonal balance. In short, every bite of ultraprocessed food rewrites part of your body’s internal instruction manual.
Q: How common is ultraprocessed food consumption, and why is it dangerous?
A: In most Western countries, over 50% of daily calories now come from ultraprocessed products such as chips, frozen meals, sweetened cereals, and soft drinks. These foods are engineered for taste, convenience, and addiction, but not for nutrition.
They contain high amounts of vegetable oils, emulsifiers, artificial sweeteners, and preservatives that cause oxidative stress, alter gut bacteria, and disrupt your body’s repair systems. The damage accumulates silently, often years before disease becomes apparent.
Q: What steps can I take to protect my DNA and health?
A: Start by changing what’s in your kitchen. Stock real foods (fresh fruit, vegetables, eggs, and homemade meals) instead of processed snacks. Build each meal around protein and fiber to stabilize blood sugar and stay full longer. Read ingredient lists carefully — shorter lists usually mean fewer additives. Plan indulgences on purpose so you can enjoy treats without losing control, and surround yourself with people who support healthy eating.
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