N-3 polyunsaturated fatty acids (n-3 PUFAs), such as eicosapentaenoic acid (EPA) and docosahexaenoic aids (DHA), are abundant in fish oil, have received increasing attention in various clinical fields. The action of n-3 PUFAs is performed as components of cell membranes or through the production of eicosanoids and docosanoids, including prostaglandins (PGs) and leukotriens (LTs). In pediatric practice, n-3 PUFAs participate in the development of visual and brain functions in infants and in the anti-inflammatory and anti-allergic functions. This paper reports the results of our clinical and animal studies concerning the effects of n-3 PUFAs on inflammatory bowel disease (IBD), allergic diseases, and development of children. Our data clearly demonstrates that n-3 PUFAs, including DHA and EPA, are effective in the treatment of IBD and allergic diseases and are involved in the development of children and even mature infants.