This experiment studied the effect of 3 different physical forms of linseed fatty acids (FA) on cow dairy performance, milk FA secretion and composition, and their relationship with methane output. Eight multiparous, lactating Holstein cows were assigned to 1 of 4 dietary treatments in a replicated 4 x 4 Latin square design: a control diet (C) based on corn silage (59%) and concentrate (35%), and the same diet supplemented with whole crude linseed (CLS), extruded linseed (ELS), or linseed oil (LSO) at the same FA level (5% of dietary dry matter). Each experimental period lasted 4 wk. Dry matter intake was not modified with CLS but was lowered with both ELS and LSO (-3.1 and -5.1 kg/d, respectively) compared with C. Milk yield and milk fat content were similar for LSO and ELS but lower than for C and CLS (19.9 vs. 22.3 kg/d and 33.8 vs. 43.2 g/kg, on average, respectively). Compared with diet C, CLS changed the concentrations of a small number of FA; the main effects were decreases in 8:0 to 16:0 and increases in 18:0 and cis-9 18:1. Compared with diet C (and CLS in most cases), LSO appreciably changed the concentrations of almost all the FA measured; the main effects were decreases in FA from 4:0 to 16:0 and increases in 18:0, trans-11 16:1, all cis and trans 18:1 (except trans-11 18:1), and nonconjugated trans 18:2 isomers. The effect of ELS was either intermediate between those of CLS and LSO or similar to LSO with a few significant exceptions: increases in 17:0 iso; 18:3n-3; trans-11 18:1; cis-9, trans-11 conjugated linoleic acid; and trans-11, trans-13 conjugated linoleic acid and a smaller increase in cis-9 18:1. The most positive correlations (r = 0.87 to 0.91) between milk FA concentrations and methane output were observed for saturated FA from 6:0 to 16:0 and for 10:1, and the most negative correlations (r = -0.86 to -0.90) were observed for trans-16+cis-14 18:1; cis-9, trans-13 18:2; trans-11 16:1; and trans-12 18:1. Thus, milk FA profile can be considered a potential indicator of in vivo methane output in ruminants.