Clomid, or Clomiphene, is a widely used fertility drug that has been in use since the early 1960s. Though it is normally well tolerated, it may cause side effects. Some of them include headaches, nausea, flashes of light, hot flashes, mood swings and abdominal discomfort. In addition, it is generally not used for more than 12 months due to an increased risk of ovarian cancer.