Phyto-oestrogens are believed to have a range of beneficial effects on predominant Western diseases. A few studies on phyto-oestrogens in milk exist and show that the composition can be affected by feeding. Therefore, the aim was to study how feeding of lucerne and grass/clover silages (GCSs) affects the concentration of phyto-oestrogens in bovine milk. Sixteen Danish Holstein cows were assigned to a 4 × 4 latin square design with four cows per treatment per period of 3 weeks. The four treatment diets were lucerne silage (LS), 2/3 lucerne silage and 1/3 maize silage (2/3LS), 1/3 lucerne silage and 2/3 maize silage (1/3LS) and GCS. Milk was collected at the end of each period and feed samples on day 6, 13 and 20 in each experimental period. Milk and pooled feed samples were analysed for the concentration of isoflavones, coumestans and lignans. The content of isoflavones was higher and the content of coumestrol lower in the GCS diet than in LS, 2/3LS and 1/3LS diets. For the LS, 2/3LS and 1/3LS diets, the concentration of coumestrol and secoisolariciresinol increased with the proportion of lucerne while the concentration of isoflavones was similar across the diets. The concentrations of the formononetin, daidzein and equol in the milk were significantly higher for the GCS diet than for the LS, 2/3LS and 1/3LS diets. In particular, the concentration of equol was 62–291 times higher for GCS. The concentration of coumestrol was significantly lower for the GCS diet compared to the LS, 2/3LS and 1/3LS diets. No pattern for the concentration of lignans was observed. In conclusion, a high concentration of isoflavones, particularly equol, and a low concentration of coumestrol were measured in the milk from the GCS diet. In contrast, a low concentration of isoflavones and a high concentration of coumestrol were measured in the milk from the LS, 2/3LS and 1/3LS diets. However, the concentration of phyto-oestrogens in bovine milk is low compared to food sources rich in phyto-oestrogens but the high concentration of equol could possibly be of therapeutic importance.