According to a study from Linkoping University in Sweden, Omega-3 fatty acids have a protective effect on allergies in children. For one year olds whose mothers had ingested fish oil during pregnancy and breastfeeding, there were considerably fewer incidences of allergic reactions compared with children whose mothers did not take the supplement. Since starting in 2005, the study comprised of 145 pregnant mothers with families at heightened risk of developing asthma and allergy. From the 25th week of pregnancy through the third month of nursing, they were asked to take nine capsules of fish oil every day. Half of them were given fish oil with high levels of omega-3 fatty acids while the other half were given a placebo in the form of a soybean pill.

The results found that children with fish-oil ingesting mothers had fewer than half as many reactions to eggs at the age of one year when compared to the placebo group. This is significant because allergic reactions to eggs early in life are strongly associated with the later development of allergic disorders like eczema and asthma.

An immunological study of the mothers' blood supported the effect of the omega-3 fats on allergy formation. The women given fish oil had less prostaglandin E2 in their blood compared to others. This substance triggers allergic immune responses, and it is known that increased concentration of omega-3 depresses its concentration.

The study leader claims, "We have been able to show that omega-3 influences the mother's immunological profile in a less inflammatory direction. Theoretically this can also affect the child's immune system, which is supported by the results of the scratch tests."

Another study looked into how changes in diet may have, especially the consumption of Omega fatty acids affect gene expression. For the past century, changes in the Western diet have altered the consumption of omega-6 fatty compared with omega-3 fatty acids.

Floyd Chilton and colleagues reported in the Journal of Biological Chemistry  that many other studies showed that changes in this ratio between the different omega acids bring about increased risk of inflammation which is associated with increased incidences of autoimmune diseases and allergies.

The research group controlled the dietary intake of omega acids of a group of 27 health participants, providing a diet more in keeping with the historical norm. They then looked at the gene levels of immune signals and cytokines (protein immune messengers), that impact autoimmunity and allergy in blood cells and found that many key signaling genes that promote inflammation were markedly reduced compared to a normal diet

This study demonstrates, for the first time in humans, that large changes in gene expression are likely an important mechanism by which these omega fatty acids exert their potent clinical effects.