5 biggest mistakes CTOs make when deciding what IP to patent

Developing an effective IP strategy for startups is a high-stakes decision that can shape funding outcomes, licensing potential, future M&A value, and even your ability to operate in a competitive space.

The core challenge? Deciding what to patent and when. A strong patent strategy requires balancing technical novelty against business priorities, understanding what technology to patent versus what to protect as trade secrets, and making smart IP decision-making choices before disclosure windows close. Unfortunately, many patent mistakes startups make stem from treating IP as an afterthought rather than building it into the product roadmap from day one.

Read on as we unpack the most common and costly mistakes in patent filing that CTOs and startups make when deciding what to patent. 

1. Delaying patent strategy until it's too late

One of the most common and damaging mistakes CTOs make is deferring patent strategy until the next funding round, product launch, or exit conversation. At early-stage companies, IP often takes a back seat to shipping products, closing customers, or getting that term sheet signed. 

But by the time the company is “ready” to think about patents, it’s often too late. In the U.S., you’re provided a “grace period” of one year from your first public disclosure to file a patent application. If you aren’t tracking those dates, you could lose the right to patent the technology. 

Even worse, most international jurisdictions require that patent applications be filed before public disclosure — meaning you could lose most international patent rights if you don’t plan ahead. Disclosures can include demos at conferences, offers for sale, investor pitch decks, public GitHub commits, blog posts, and sometimes even customer pilots if NDAs aren’t airtight. 

Once an invention is disclosed, it may no longer be eligible for patent protection, meaning you lose exclusivity over the very technologies that differentiate your company.

Pro tip: A well-timed provisional application can preserve rights while the product and business strategy evolve. They give you 12 months to refine claims, test commercial traction, and layer in improvements without locking yourself into a full non-provisional too early.

2. Treating IP as a checklist, not a strategic asset

There’s a big difference between “having patents” and “having a patent strategy.” Without a deliberate link to product roadmap, competitive landscape, and future fundraising or exit goals, patents can end up being irrelevant.

Not all inventions are worth patenting. Some are better kept as trade secrets. Others may seem novel but aren’t aligned with what gives your company a competitive advantage. I’ve seen portfolios bloated with patents that cover deprecated features, side projects, or inventions that will never be commercialized, while the core differentiator remains unprotected.

Strong IP strategy for startups requires disciplined IP decision-making. Here are the hard questions that guide what to patent:

• What parts of the technology are central to long-term differentiation from competitors?
• Which of those are actually patentable?
• Which are valuable, or are they related to the ways the company generates revenue?
• When is the right time to file, so that it aligns with product development and fundraising cadence while staying ahead of disclosure dates?

3. Drafting without foresight

Another common mistake CTOs make is filing a patent without understanding what makes a good patent. How is it scoped, structured, and sequenced? 

Poor drafting choices can quietly undermine the entire value of a filing:

• Applications that are too narrow are easy to design around or only protect a single implementation, leaving the competitive moat wide open.
• Applications that are too broad mean the application may never get granted, burning time and legal budget in endless rounds of prosecution.
• Applications that are too dense, where you cram multiple inventions into a single draft, can increase prosecution expenses when it comes to splitting off valuable claim sets through divisionals and continuations.

Then there’s the issue of unintentional self-sabotage. It’s common to disclose multiple aspects of a technology in a single filing, thinking it saves cost. But that disclosure can later become your own prior art, preventing you from getting additional patents on improvements, variations, or related functionality in the future.

So, instead of just filing as many patents as quickly as possible, treat your applications as chess moves in a multi-year IP roadmap. That means:

• Mapping filings to product phases, not just current functionality.
• Sequencing inventions to preserve optionality for future filings.
• Scoping claims to balance near-term defensibility and long-term expansion.
• Keeping detailed invention disclosures internally, even for ideas you’re not ready to file on.

4. Patenting what should’ve been a trade secret

Not every competitive advantage belongs in a patent. In some cases, filing can do more harm than good, especially when the disclosed material offers long-term value precisely because it’s hard to reverse-engineer or replicate.

CTOs often assume that if something is novel and important, it must be patented. But that mindset can lead to exposing critical algorithms, internal tooling, or optimization techniques that would be far better protected as trade secrets. Once published, a patent becomes part of the public domain, meaning competitors gain insight without having to innovate.

Knowing how to decide what to patent versus what to keep confidential is critical IP decision-making for any CTO. Ask yourself and the team:

• Can the technology be reverse-engineered? If it’s not visible to users or customers, there may be no need to disclose it.
• Could you detect whether the same technology is being used by a competitor? If not, enforcing the patent becomes unfeasible.
• Will you be forced to disclose the technology for other reasons (e.g., regulatory compliance or fundraising)? If so, filing a patent can help you maintain exclusivity while still disclosing the information.
• Can the same claims be supported with a less detailed description? Don’t give away more than you need to.
• Would disclosure meaningfully erode our competitive edge? If yes, consider holding it back.

In many cases, the right approach is hybrid: patent the externally visible mechanism or output, and retain the underlying systems, methods, or enhancements as proprietary know-how.

5. Underestimating the impact of inventorship and assignment errors

Many CTOs think of patents as technical documents first, legal assets second. But from the perspective of investors, acquirers, or enforcement, a patent is only as strong as the chain of title behind it.

One of the most overlooked risks is improper or incomplete assignment of rights. If the inventors listed on the application haven’t signed assignment agreements transferring their rights to the company, the company doesn’t fully own the patent, even if it paid for the filing. If your patents are not owned by your company, all it takes is one disgruntled employee withholding their signature from an assignment document to cause serious issues.

Inventorship errors are another subtle but dangerous issue. Patent law requires that all true inventors be named, and no one else. In some cases, patents have been ruled invalid because a founder left the company and was not included on the list of inventors.

Patentext Origin: The best IP strategy for startups solution

For CTOs, the costliest patent mistakes rarely come from the USPTO; instead, they come internally. Missed invention windows, unclear documentation, scattered embodiments, and unprioritized disclosures can quietly erode future patentability long before outside counsel ever enters the picture. And once strategy falls out of sync with the product roadmap, it becomes harder (and far more expensive) to fix later.

Patentext Origin helps teams build a real system around these decisions. Our platform surfaces the most inventive elements in your product, pulls out patent-worthy variations hidden in your documentation, and guides your team through structuring disclosures in a way your attorney can immediately act on. With clearer inputs, your IP strategy becomes easier to prioritize against business goals (and far less dependent on ad-hoc conversations or guesswork).

Join the waitlist for Patentext Origin to lock in 20% off lifetime pricing.

‍

Disclaimer: This article is for informational purposes only and does not constitute legal advice. Patent laws are complex and vary by jurisdiction. For personalized guidance, consult a qualified patent attorney or agent.