Any side effects of clomid, (clomiphene) that become the long effect years later?

Unlikely: Most side effects of Clomid (clomiphene) are short-term = headache, hot flushes, irritability, bloating, ovarian cysts. Theoretical long-term risk may include ovarian cancer. However, risk of ovarian ca is more likely related to patient population using clomid, (clomiphene) mainly women who do not have children or have their first child at an older age, which are known risk factors for ovarian ca.

Generally not, but: There are some concerns it may increase the risk of ovarian cancer. Aside from this, no.