The statement of claim filed by Bruce McKenzie says his 18-year-old daughter, Marit, died after taking a drug called Diane-35.
The statement says she suffered four cardiac arrests, a pulmonary embolism and a brain hemorrhage.
It also says the drug store chain did not tell her that Diane-35 should be discontinued three to four months after signs of acne have completely resolved.
Tammy Smitham, a vice-president of Shoppers, issued a statement extending condolences to the family and calling the death "a tragedy."
She says the company's priority is the health of its customers and their families.
"As partners in Canada's health care system, pharmacists work together with Health Canada, drug manufacturers and doctors to inform and counsel patients on the appropriate use and safety of their medications," said Smitham.
"Given that the matter is subject to litigation, we cannot provide any further comment at this time."
Health Canada has issued several advisories over the past few years on the risks associated with Diane-35, including blood clots.
The agency has noted Diane-35 has been prescribed as birth control although that's a use the manufacturer has not been granted approval for by Health Canada.
Late last month, Health Minister Rona Ambrose asked the drug's manufacturer to fund a physician's education initiative to provide guidance on the drug's use.
The statement of claim says Marit McKenzie started taking Diane-35 more than a year before she died.
It alleges Shoppers was negligent in "continuing to renew Marit's prescription in the face of the Health Canada warnings" and failing to provide warnings "equivalent to those provided by other pharmacies."
The statement of claim contains allegations that have not been proven in court.
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