The most common cause of low omega-3 levels is simply not eating enough of the foods that contain them, particularly fatty fish. An estimated 76 percent of people worldwide fall short of recommended intakes of the two most important omega-3 fats: EPA and DHA. But diet isn’t the only factor. Your genetics, other fats in your diet, alcohol use, and certain medical conditions can all drive your levels down or prevent your body from using omega-3s effectively.
Not Enough EPA and DHA in Your Diet
Your body cannot make omega-3 fatty acids from scratch. You have to get them from food. The two forms that matter most for your health, EPA and DHA, come almost exclusively from marine sources: salmon, mackerel, sardines, herring, anchovies, and other fatty fish. Shellfish and algae also provide meaningful amounts. If you rarely eat these foods, your levels will reflect that.
There’s an important distinction between types of omega-3s. Plant foods like flaxseed, chia seeds, and walnuts contain a different form called ALA. Your body can convert ALA into EPA and DHA, but the conversion is remarkably inefficient. In healthy young men, only about 8 percent of ALA gets converted to EPA and somewhere between 0 and 4 percent becomes DHA. Women of reproductive age do better, converting roughly 21 percent to EPA and 9 percent to DHA, likely due to the influence of estrogen. Even in the best-case scenario, relying solely on plant-based omega-3s makes it difficult to reach the levels associated with health benefits.
Too Much Omega-6 Fat in Your Diet
Omega-6 fats and omega-3 fats compete for the same enzymes in your body. These enzymes (called desaturases) are the machinery that converts shorter-chain fats into their longer, more active forms. The enzymes naturally prefer omega-3s over omega-6s. But when your diet is flooded with omega-6 fats, which is typical of Western diets heavy in vegetable oils like soybean, corn, and sunflower oil, the sheer volume of omega-6 overwhelms those enzymes and crowds out omega-3 conversion.
This means that even if you’re eating some ALA from plant sources, a high intake of omega-6 fats can suppress your body’s ability to turn that ALA into useful EPA and DHA. Reducing your omega-6 intake by cooking with oils like olive oil and cutting back on highly processed foods can help your body make better use of the omega-3s you do consume.
Genetic Differences in Omega-3 Processing
Not everyone converts omega-3s at the same rate, even with identical diets. Variations in two genes, FADS1 and FADS2, directly affect how efficiently your body runs the enzymes that process fatty acids. Researchers studying a genetically homogeneous island population (where everyone ate roughly the same diet) found that specific gene variants significantly altered people’s fatty acid levels. Some variants reduced the activity of the key conversion step, meaning those individuals produced less of the long-chain fatty acids their bodies needed.
A separate analysis identified a variant in the FADS2 gene’s promoter region that influences how much of the enzyme gets produced in the first place. If you carry certain combinations of these variants, you may need more preformed EPA and DHA from fish or supplements because your body is less capable of manufacturing its own supply from plant-based precursors.
Fat Malabsorption Conditions
Omega-3 fatty acids are fats, so any condition that impairs fat absorption will also impair omega-3 uptake. A wide range of gastrointestinal and organ-related diseases can cause this problem.
Damage to the small intestine lining is one common mechanism. Conditions that cause this kind of damage include celiac disease, Crohn’s disease, ulcerative colitis, small intestinal bacterial overgrowth (SIBO), short bowel syndrome, and tropical sprue. Infectious diseases like Whipple’s disease can do the same, as can radiation therapy, chemotherapy, and chronic heavy alcohol use.
Problems with the pancreas, liver, or gallbladder represent another category. Your pancreas produces enzymes that break down fats, and your liver and gallbladder supply bile, which helps dissolve them. Pancreatic insufficiency, cystic fibrosis, bile duct blockages, gallbladder disease, and liver disease can all reduce your ability to absorb dietary fats. Diseases of the lymphatic system, such as intestinal lymphangiectasia, block the vessels that transport absorbed fats into your bloodstream, creating yet another barrier. If you have any of these conditions and notice symptoms like oily or greasy stools, your fat absorption is likely compromised, and your omega-3 levels may be affected.
Alcohol’s Effect on Omega-3 Levels
Alcohol actively depletes DHA, the omega-3 fat most concentrated in your brain. Research shows that ethanol lowers DHA levels while simultaneously raising omega-6 levels, which shifts the overall ratio in an unfavorable direction. This is particularly damaging in the brain, where DHA plays a critical role in the flexibility and signaling capacity of nerve cell membranes. The DHA depletion caused by alcohol impairs a specific type of learning-related brain activity in regions like the hippocampus and prefrontal cortex.
Animal and cell studies suggest that enriching the diet with omega-3s can counteract some of alcohol’s damaging effects, including reversing the DHA deficit in brain tissue. But the core point remains: regular or heavy drinking is an independent driver of lower omega-3 status, even if your dietary intake is otherwise reasonable.
How Low Omega-3 Levels Are Measured
The most widely used measure is the Omega-3 Index, a blood test that reports the percentage of EPA and DHA in the membranes of your red blood cells. This reflects your average intake over the past two to three months, similar to how an HbA1c test reflects blood sugar over time.
An Omega-3 Index between 8 and 11 percent is considered the target range. Below 4 percent is the lowest tier studied, and in large population studies, people with levels near or below that mark had roughly 1.5 times the total mortality risk compared to those in the 8 to 11 percent range. The relationship between the index and mortality risk is continuous, meaning every incremental increase across that spectrum is associated with some degree of benefit.
True clinical omega-3 deficiency, with outright symptoms like scaly skin or impaired wound healing, is extremely rare in the United States and other developed countries. There are no formally established blood thresholds below which specific bodily functions are known to fail. What most people experience instead is suboptimal levels: not low enough to cause obvious symptoms, but low enough to miss the protective benefits that higher levels provide. That distinction matters because you can have a meaningful omega-3 shortfall without any obvious signs pointing to it.
Why Supplement Quality Isn’t a Major Factor
One concern people sometimes have is whether low-quality or oxidized fish oil supplements might explain persistently low omega-3 levels. Research on this has been reassuring. A randomized crossover study comparing oxidized and non-oxidized cod liver oil found no significant differences in how much EPA or DHA made it into the bloodstream. A longer seven-week study reached the same conclusion: oxidized fish oil delivered the same measurable omega-3 levels as fresh oil. While there may be other reasons to prefer high-quality supplements (taste, fewer fishy burps, lower levels of potentially harmful oxidation byproducts), poor absorption from a rancid product is unlikely to be the reason your levels aren’t rising.
If you’re supplementing and your levels remain low, the more likely explanations are insufficient dosing, a genetic profile that limits conversion (if you’re taking ALA-based supplements rather than EPA/DHA directly), a malabsorption condition, or competing factors like high omega-6 intake or alcohol use.