A placebo-controlled, double-blind study was conducted to investigate the effects of seed and pulp oils of sea buckthorn (Hipphophae rhamnoides) on atopic dermatitis. Linoleic (34%), alpha-linolenic (25%), and oleic (19%) acids were the major fatty acids in the seed oil, whereas palmitic (33%), oleic (26%), and palmitoleic (25%) acids were the major fatty acids in the pulp oil. The study group included 49 atopic dermatitis patients who took 5 g (10 capsules) of seed oil, pulp oil, or paraffin oil daily for 4 months. During follow-up dermatitis improved significantly in the pulp oil (P < 0.01) and paraffin oil (P < 0.001) groups, but improvement in the seed oil group was not significant (P = 0.11). Supplementation of seed oil increased the proportion of alpha-linolenic acid in plasma neutral lipids (P < 0.01), and increases of linoleic, alpha-linolenic, and eicosapentaenoic acids in plasma phospholipids were close to significant (0.05 < P < 0.1). Pulp oil treatment increased the proportion of palmitoleic acid (P < 0.05) and lowered the percentage of pentadecanoic acid (P < 0.01) in both plasma phospholipids and neutral lipids. In the seed oil group, after 1 month of supplementation, positive correlations were found between symptom improvement and the increase in proportions of alpha-linolenic acid in plasma phospholipids (Rs = 0.84; P = 0.001) and neutral lipids (Rs = 0.68; P = 0.02). No changes in the levels of triacylglycerols, serum total, or specific immunoglobulin E were detected. In the pulp oil group, a significant (P < 0.05) increase in the level of high density lipoprotein cholesterol, from 1.38 to 1.53 mmol/L was observed.