Secondary Patents: How Brands Extend Market Exclusivity in Pharmaceuticals

What Are Secondary Patents?

Secondary patents aren’t about the medicine itself-they’re about how it’s made, taken, or used. While the primary patent protects the active chemical ingredient (like ibuprofen or metformin), secondary patents cover everything else: the shape of the pill, the time it releases the drug, the way it’s mixed with other chemicals, or even a new disease it can treat. These aren’t new drugs. They’re tweaks. But in the pharmaceutical world, those tweaks can mean billions in extra revenue.

Take Nexium. Its active ingredient, esomeprazole, was originally part of Prilosec. Prilosec’s primary patent expired in 2001. But AstraZeneca had already patented the single-enantiomer version-esomeprazole-as a new compound. That’s a secondary patent. Even though it’s chemically almost identical, the FDA allowed it to be listed as a new drug. Sales of Nexium jumped to $5 billion a year, while generic Prilosec flooded the market. The difference? One patent, extended by eight years.

How Secondary Patents Work

Pharmaceutical companies file secondary patents at every stage of a drug’s life. Some are filed before approval. Others come years later, after the drug is already on the market. The goal? Delay generic competition as long as possible.

There are over a dozen types of secondary patents recognized globally. The most common ones include:

• Formulation patents: Protect how the drug is delivered-slow-release tablets, liquid suspensions, patches. AstraZeneca’s Nexium is one example.
• Method-of-use patents: Cover new conditions the drug can treat. Thalidomide was originally a sleep aid. Later, it got patents for leprosy and multiple myeloma.
• Polymorph patents: Protect different crystal structures of the same molecule. GlaxoSmithKline used this to delay generics for Paxil by four years after the main patent expired.
• Combination patents: Cover a drug paired with another. For example, a blood pressure pill that combines two active ingredients into one tablet.
• Prodrug patents: Protect a version of the drug that turns into the active form inside the body.

These aren’t just legal tricks. They’re strategic moves built into the business model. Companies spend $12-15 million per secondary patent application. They hire teams of patent lawyers, scientists, and marketers to coordinate timing. The goal? Launch the new version just before the old one goes generic.

The Patent Thicket Strategy

One drug doesn’t have one secondary patent. It has dozens. Sometimes over a hundred.

Humira, AbbVie’s blockbuster arthritis drug, had 264 secondary patents by 2023. The primary patent expired in 2016. But because of the thick wall of secondary patents-covering delivery devices, dosing schedules, manufacturing methods-generic versions couldn’t enter until 2023. During that time, Humira generated $20 billion in annual sales. Without those patents, generics would have cut prices by 80% within months.

This is called a “patent thicket.” It’s not one patent blocking competition. It’s a maze. Generic manufacturers have to challenge each one in court. Each challenge costs $15-20 million. Many run out of money before they get to the end.

The FDA’s Orange Book lists only certain types of patents-mainly formulation and method-of-use. But companies keep dozens of others hidden. These are “reserve patents,” filed just in case a generic challenger clears the listed ones. It’s like having backup keys to a locked door.

Who Benefits? Who Pays?

The pharmaceutical industry says secondary patents drive innovation. They point to improved safety, easier dosing, fewer side effects. The American Cancer Society credits secondary patents for reducing chemotherapy side effects by 37% in some cases.

But critics call it “evergreening.” A 2016 Harvard study found only 12% of secondary patents delivered real clinical improvements. The rest? Minor changes that don’t help patients-but keep prices high.

Patients pay the price. Pharmacy benefit managers like Express Scripts say secondary patents raise their costs by 8.3% each year. Doctors report “product hopping”-when companies push patients to switch to the new version right before generics hit. One California physician told Medscape: “Patients get confused. They think the new pill is better. It’s not. It’s just more expensive.”

And it’s not just patients. Governments pay too. Medicare and Medicaid spend billions more because of delayed generics. The 2022 Inflation Reduction Act in the U.S. started letting Medicare challenge some secondary patents. It’s a sign things are changing.

Global Differences: What’s Allowed Where

Not every country lets pharmaceutical companies play this game the same way.

In the U.S., the Hatch-Waxman Act of 1984 created the system that made secondary patents possible. It gave brand-name companies 30 months of automatic delay if a generic challenged a patent. That’s why U.S. drug prices stay high.

India doesn’t. Section 3(d) of its 2005 patent law says: no patent for a new form of an old drug unless it shows significantly better effectiveness. Novartis tried to patent a new crystal form of Gleevec. India rejected it. Generic versions hit the market in 2011. The drug cost $2,600 a month in the U.S. In India? $200.

Brazil requires health ministry approval before a patent can be enforced. The European Union demands “significant clinical benefit” for some secondary patents. These rules aren’t perfect, but they keep prices lower.

That’s why companies file secondary patents everywhere-but only enforce them where the rules let them.

The Future of Secondary Patents

Secondary patent filings have grown 7.2% a year since 2010. But pressure is mounting.

Courts are getting stricter. In 2023, the Federal Circuit ruled in Amgen v. Sanofi that broad antibody patents were too vague. That could limit future secondary patent claims.

Regulators are watching. The European Commission’s 2023 Pharmaceutical Strategy targets patent thickets as a barrier to generic access. The WHO says secondary patents are the top legal reason generic medicines are delayed in 68 low- and middle-income countries.

Some experts predict a shift. By 2027, companies may need to prove their secondary patents actually improve patient outcomes-not just extend profits. That could mean fewer low-value patents and more real innovation.

For now, though, the system still favors the big players. Pfizer alone holds over 14,200 active secondary patents. The top 10 drugmakers control 73% of them.

It’s not illegal. It’s just the rules as they stand. And until those rules change, brands will keep using secondary patents to stretch exclusivity-long after the original invention has run its course.

How Generic Manufacturers Fight Back

Generic companies don’t sit idle. They file what’s called a Paragraph IV certification when they challenge a listed patent. In 2022, 92% of secondary patents in the FDA’s Orange Book got challenged.

But winning is hard. Only 38% of those challenges succeed in court. Why? Because the burden of proof is on the generic company. They have to show the patent is invalid-either because it’s obvious, or it wasn’t invented, or it’s too broad.

Some generics team up. Others wait. They let the first challenger go to court. If they lose, they wait for the next opportunity. It’s a long game. One company told the Generic Pharmaceutical Association: “We don’t try to beat every patent. We wait for the one that cracks.”

What Patients Should Know

If your doctor prescribes a new version of a drug you’ve been taking-ask why. Is it better? Or just newer? Is it covered by insurance? Or is it more expensive because the old one just went off-patent?

Many times, the old generic still works just fine. The new version might be slightly easier to swallow. But it won’t cure more. It won’t work faster. It’s just protected by another patent.

Ask your pharmacist if a generic version is available. Ask your insurer if they cover the cheaper option. You’re not being difficult. You’re being informed.