The objective of this study was to examine the effects of whole flax seed (FS) and flax oil (FO) supplementation on digestion, ruminal fermentation, and milk fatty acid (FA) profile of dairy cows fed high-forage (HF) or high-concentrate (HC) diets. Four ruminally lactating cows were used in a 4 × 4 Latin square design with dietary treatments arranged as a 2 × 2 factorial. High forage and HC basal diets were formulated by varying the proportions of grass and corn silages, as well as those of corn grain and soybean meal. The basal diets were fed for ad libitum intake, and supplemented with either FS or FO at the feeding rate of 2.0 and 0.7 kg/d, respectively. The forage:concentrate (F:C) ratios of the total diets (including top dressed FS or FO) were 700:300 and 300:700 on a dry matter (DM) basis for HF and HC, respectively. Increasing the concentrate proportion in the diet reduced ruminal pH, shifted volatile fatty acid (VFA) pattern toward more propionate and less acetate, and decreased protozoal numbers. These changes in ruminal fermentation resulted in a decrease of in sacco effective ruminal degradability (ERD) of acid detergent fiber (ADF) and neutral detergent fiber (aNFD) of grass silage. Despite alterations in rumen function, no interactions occurred between the proportion of concentrate in the diet and flax supplementation. Replacing FS with FO in the diet had no effect on dry matter intake (DMI) and ruminal fermentation characteristics, but increased organic matter (OM) digestibility and milk yield. An interaction between F:C and flax supplement was observed for the milk fat ratio of trans-11 18:1 to trans-10 18:1, which increased when FO replaced FS in HF diets, while the opposite was observed with HC diets. Feeding FS increased milk fat content and transfer efficiency of cis-9, cis-12, cis-15 18:3, the major FA present in flax, and decreased the concentration of trans intermediates of ruminal biohydrogenation as compared with FO.