Desogestrel is a prodrug and is rapidly metabolized in the intestinal mucosa and on first pass through the liver to its active metabolite, etonogestrel (3-ketodesogestrel). Following oral administration, the relative bioavailability for desogestrel is approximately 84%. Desogestrel also exhibits high selectivity for the progesterone receptor and low and rogenic activity, and it does not diminish the beneficial effects of estrogen on the lipid profile.

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