Effects of phytoestrogen isoflavones in Berseem clover on hormonal balance during early pregnancy and fertility of heifers were studied. Holstein heifers (n=26) were divided into two equal homogenous groups. Heifers in the first group (Clover-fed group) were fed Egyptian clover (Trifolium alexandrinum) as oestrogenic roughage; whereas the heifers in the second group (Silage-fed group) were fed maize silage. Concentrations of four isoflavone aglycones (genistein. Daidzein, biochanin A and formononetein) were determined in the two roughages. Treatment lasted for 20 consecutive weeks (5 months) during which blood samples were collected biweekly for determining the metabolic profile of heifers. Heifers were subjected to oestrous synchronisation using a double prostaglandin F2α (PGF2α) based protocol, 14days apart (week 10 and 12), and were artificially inseminated 12h following detection of overt signs of oestrus. Concentrations of serum oestradiol (E2) and progesterone (P4) on the day of insemination (Day 0) and on Days 7, 14 and 21 post-insemination (early pregnancy) were determined and P4 to E2 ratio was calculated. Clover had greater total isoflavone content than maize silage. The dominant isoflavone detected in Berseem clover was biochanin A, whereas the least was formononetein. Metabolic profile was not affected (P>0.05) by the type of roughage and was in the same trend in both experimental groups. The overall mean concentration of serum E2 was greater (P<0.05) in the clover-fed group than in the silage-fed group. The overall mean concentration of serum P4 was less (P<0.05) in the clover-fed group than in the silage-fed group. During the period of early pregnancy (from Day 7-21 post-insemination) the concentration of serum P4 increased in the silage-fed group, however, no change was observed in the clover-fed group. The overall mean of P4 to E2 ratio was greater (P<0.001) in the silage-fed group compared with that in the clover-fed group. Heifers fed clover had a lesser (P=0.054) conception rate and a greater (P=0.062) percentage of heifers returning to oestrus than silage-fed heifers. In conclusion, isoflavones in Berseem clover apparently disturbed hormonal balance during early pregnancy leading to a reduction in the fertility of heifers.