Six embryos were created and frozen in 2001 with her then partner, Howard Johnston, before she had her ovaries removed to treat a pre-cancerous condition.
At the time Ms Evans considered whether to explore other means of having her eggs fertilised to guard against the possibility of her relationship ending, but he assured her that would not happen.
Under UK law both people in the process must given written permission for the treatment and it is possible to withdraw this at any time before the fertilised embryos are implanted in the woman's uterus.
In May 2002 the relationship ended and Mr Johnston told the clinic he no longer gave his permission for the embryos to be used and asked for them to be destroyed.
Ms Evans claimed that not being able to use the embryos breached her human rights, including the right to respect for private and family life (article eight) and the prohibition of discrimination (article 14). Ms Evans also argued that it would breach the embryo's right to life (article two).
But in its judgement today, the ECHR said the embryos did not have a right to life under the terms of article two and she could still become a mother as she could adopt a child or give birth to a child originally created in vitro from donated gametes.
The decision follows failed appeals at the UK's high court and court of appeal and means the embryos will now be destroyed.
Ms Evans has said that she is "distraught" at the decision and it is "very hard" for her to accept.
Speaking after the ruling, Mr Johnston said that he is "very relieved" and feels that "commonsense has prevailed".
"Of course I'm sympathetic to the situation that [Ms Evans] is in but I want to be able to choose as and when I become a parent," he added. "The [UK] has been proven to be correct."
Dr Tony Calland, chairman of the British Medical Association's medical ethics committee, commented: "We have every sympathy for Natallie Evans, and understand why she has challenged the law.
"However, we welcome the fact that the European court has supported the principle of consent from all parties. Having a child is a life-long undertaking to which both partners should be fully committed."
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