This study examined (1) if fatty acids in bovine hair are influenced by dietary energy levels and (2) if the relationship between energy availability and fatty acids in hair persists across breeds and farms. Sixty-two and 59 Fleckvieh (Simmental), and 55 German Holstein cows from three farms, respectively, were fed two levels of energy concentration of roughage (6.1 and 6.5 MJ net energy for lactation/kg dry matter) and two levels of concentrate supply (150 and 250 g/kg energy-corrected milk). The average body weight was 727 kg (Simmental) and 668 kg (Holstein). The average lactation number was 3.1. Hair samples were taken in lactation weeks 4 and 8. In Simmental cows, a lower energy deficit due to a relatively higher energy intake from high energy concentration of the roughage was associated with higher C18:2n-6 and C18:3n-3 contents in hair at week 8. In cows from all three farms, higher energy intake between lactation weeks 2 and 6 correlated with higher content of C18:2n-6 in hair samples taken in lactation weeks 4 and 8. No correlation was found for C12:0. These results provide the first evidence that increased energy intake increases the contents of C18:2n-6 in hair.