Fatty acid composition was studied in breast milk of allergic and non-allergic mothers, focusing in particular on concentrations of the n-6 and n-3 long-chain polyunsaturates (LCP) in relation to maternal allergy. Milk samples were obtained from 168 mothers with asthma or inhalant allergies and 107 mothers without asthma and inhalant allergies, between 2 and 35 weeks after delivery. Mean values of fatty acid concentration (weight% of total fatty acids) were estimated for individual fatty acids, for groups of fatty acids and for the metabolic index (the ratio between the sum of n-6 polyunsaturates and linoleic acid). For the most relevant fatty acids, the association with maternal allergy was subsequently analyzed in more detail using multiple regression analysis. The metabolic index in breast milk was significantly lower in the allergic than in the non-allergic mothers, but no significant differences were observed in the concentrations of any of the n-6 fatty acids. Also concentrations of the n-3 fatty acids and nearly all other fatty acids were similar in allergic and non-allergic mothers' breast milk. No differences in fatty acid concentrations were observed between mothers with asthma and mothers with single or with multiple inhalant allergies. Our data suggest that differences in fatty acid composition between breast milk of allergic and non-allergic mothers are small and are unlikely to be responsible for the differential effects of breastfeeding by allergic and non-allergic mothers that have been observed in some studies.