During the transition period, cows exhibit reduced immune function that can lead to postpartum disease and reduced fertility. Dietary fatty acids (FA) modulate immune function. This study determined the effects of feeding a supplement high in n-3 (omega-3) FA on milk production, FA concentration in milk and plasma, postpartum disease and fertility. Six sequential, 60-d periods (n = 3 control (C), n = 3 treated (FL)) were conducted over 12 mo on a commercial dairy. A subset of cows (2+ lactations) and heifers (1st lactation) receiving the C (n = 292) or FL (n = 271) diets for the entire transition period were used. Diets were fed starting ~3 weeks pre-calving and for ~3 weeks after calving. The C diet was isonitrogenous and isocaloric to the FL diet, which contained a commercial flaxseed supplement (LinPROR) formulated to 3% of dry matter intake. Individual cow production, health and fertility data were collected. Blood was taken from a subset of cows and heifers (n = 12/period) at entrance into the close-up pen, the week of calving and for 2 following weeks. Plasma and milk were analyzed for FA content. Data were analyzed using the MIXED procedure of SAS with repeated measures or proc GLIMMIX, with fixed effects of treatment and lactation and random effects of cow within treatment. Seasonal effects were accounted for by blocking. Both milk and plasma total n-3 concentration was greater (P < 0.01) in the FL group, while the n-6:n-3 ratio was lower (P < 0.01). Milk yield tended to be greater in the FL group at 5 (P = 0.06) and 10 weeks (P = 0.1) postpartum. Milk fat and protein percent were greater (P < 0.01) in the FL group during the first month of lactation. First service conception rates in cows (C 54% vs. FL 55%) and heifers (57% vs. 67%) did not differ nor did pregnancy loss. Incidence of postpartum disease did not differ between groups. In summary, the FL diet increased n-3 FA in milk and plasma and tended to increase milk yield while having no detrimental effect on conception rates, embryo loss or disease postpartum.