Probiotic therapy is a new, successful approach to alleviating allergic symptoms. In this study, our aim was to investigate whether the positive results obtained with probiotic therapy would be associated with the differential absorption and utilization of dietary PUFA. 15 infants referred to a pediatric clinic on the basis of atopic eczema were weaned to Bifidobacterium Bb-12 or Lactobacillus GG supplemented infant formula, or to the same formula without probiotics (randomized, placebo-controlled, double blind study design). In plasma neutral lipids, alpha-linolenic acid (18:3 n-3) proportions were reduced by the probiotic supplementation. In phospholipids, Lactobacillus GG supplemented formula did not influence alpha-linolenic acid proportions, while Bifidobacterium Bb-12 supplemented formula increased the proportion of alpha-linolenic acid; from 0.13 +/- 0.03 to 0.24 +/- 0.03 (mean +/- SEM) (P = 0.002). These results show that some physiological effects of probiotics may be associated with physiological interactions between probiotics and dietary PUFA.