NIH SBIR Phase II Application Guide

Start With Phase I Results

When preparing your NIH SBIR Phase II application, your starting point must be the progress and outcomes of your Phase I award. Reviewers expect clear evidence that Phase I was successful—not only in proving technical feasibility but in setting the stage for commercial development. This narrative forms the backbone of your entire proposal.

Begin by revisiting your original Phase I Specific Aims. For each, assess how completely it was achieved and what concrete results you can now present. Where possible, use measurable indicators: data from experiments, prototype performance benchmarks, completed milestones, or user feedback. Include any publications, presentations, or intellectual property filings resulting from Phase I, even if brief.

Your review should also highlight technical or market risks that remain. Acknowledging these openly—paired with a plan for how Phase II will address them—adds credibility. If any aim was only partially met, explain why, and describe what adjustments you’ve made for Phase II. NIH values honest, thoughtful evaluation.

Commercial potential is just as important. Did your Phase I results suggest there’s a path to market? If you developed a prototype, how well did it perform? Did you engage end-users, conduct preliminary market research, or identify potential adopters? Summarize any traction you’ve gained with partners or investors—even soft signals like expressions of interest.

The goal is to create a clear, evidence-based narrative: Phase I confirmed feasibility, and Phase II will build on that foundation toward a viable product or service. You’ll revisit some of this in your Research Plan and Commercialization Plan, but this internal review sets the tone and guides your next steps.

Confirm IC Alignment and Talk to Your PO

Before you begin writing your Phase II application, take time to confirm that your project still aligns with the NIH Institute or Center (IC) that funded your Phase I. Each IC has its own research priorities, budget caps, waiver topics, and follow-on funding options. Confirming alignment now can save you from a misrouted application or unfavorable review panel assignment later.

Your first step should be scheduling a discussion with your NIH Program Officer (PO)—specifically, the SBIR/STTR PO at the IC that funded your Phase I. NIH encourages this interaction, and some ICs require it before accepting Phase II applications.

Prepare a one-page Specific Aims summary or concept memo before your conversation. This document should briefly outline:

• The key outcomes of your Phase I work
• Your high-level goals for Phase II
• Any notable changes in technical scope or commercial direction

Send it to your PO ahead of time. This makes the conversation focused and productive.

During the meeting, ask:

• Does your proposed Phase II project still fit the IC’s current topic interests?
• Are there any updated budget policies (e.g., new caps or waiver requirements)?
• Should you apply through the parent omnibus FOA, or is there a more appropriate targeted solicitation?
• What study section is likely to review your application, and are there any recommendations for tailoring your proposal?
• Does your proposed budget exceed the standard cap—and if so, is your topic eligible for a waiver?

If your work now overlaps multiple ICs, your PO can also advise on whether to request dual assignment or a secondary review. This is typically done in the cover letter you submit with your application.

Timing is critical. You should initiate this conversation at least two months before the submission deadline. That window gives you time to adjust your scope, FOA selection, and budget strategy based on the PO’s guidance.

Schedule your PO discussion 2+ months before the deadline.
Late contact may limit your options for FOA selection, budget waivers, or IC reassignment.

If you anticipate needing a Phase IIB award in the future, this is also the time to ask whether your IC participates in that program. Some do; others do not. Phase IIB is not something you can switch into later—it must be anticipated and aligned from the start.

Finally, use this conversation to confirm the application deadline and any upcoming policy shifts that could affect your submission. NIH updates policies frequently, and your PO can clarify what applies to you.

This early strategic check-in ensures you’re not just compliant, but competitive.

Write the Phase I Progress Report

The Phase I Progress Report is a required element of your NIH SBIR Phase II application. It’s the narrative proof that your Phase I work established a sound foundation for further development—and it must be built into your Research Strategy. NIH reviewers read it closely to assess whether your proposed Phase II activities are justified and feasible.

Start by stating the Specific Aims from your original Phase I proposal. For each aim, summarize what was accomplished. Use quantitative outcomes whenever possible:

• Performance data from prototypes
• Results from pilot tests or assays
• Milestones met or exceeded
• Feedback from target users or advisors

If certain aims were not fully met, explain why. NIH expects transparency. Did the approach change based on early results? Did technical barriers arise? Reviewers value adaptive learning if you show how insights from Phase I shape your Phase II approach.

Next, describe the technical significance of your findings. For example, did you overcome a known limitation in the field? Prove a concept that competitors had not? De-risk a complex integration?

Then, list tangible achievements:

• Patents filed or issued
• Publications, posters, or white papers
• Beta versions or early prototypes
• Regulatory conversations initiated (e.g., FDA pre-submission)

Finally, summarize the current state of your technology or product. Is it a validated prototype, alpha software, or tested compound? NIH requires you to describe its stage of development using standard terminology (e.g., “in preclinical testing,” “bench-top prototype,” etc.). If your work involves a regulated product, mention progress toward approvals or classifications (e.g., 510(k) or IND discussions).

This report is part of your Research Strategy and counts toward its page limit.
Do not submit it as a separate attachment unless specifically required by your FOA.

It’s helpful to include limited visuals—data charts, prototype photos, or diagrams—if allowed by your FOA. These make your accomplishments more concrete and memorable.

Remember, the goal of this section is not just to document activity—it’s to persuade reviewers that Phase I demonstrated feasibility, and that your team is capable of executing Phase II. Write with confidence, but stay factual.

By the end of this report, reviewers should believe three things:

1. You made meaningful technical progress.
2. Your innovation has matured to a point where deeper development is warranted.
3. You’re the right team to deliver Phase II results that move the technology toward the market.

Build a Targeted Research Plan

The Research Plan is the scientific heart of your NIH SBIR Phase II application. Reviewers will score it based on significance, innovation, and feasibility—so each part must be tightly written, well-supported, and aligned with your IC’s mission.

The Research Plan includes:

• Specific Aims (1-page summary)
• Research Strategy (12-page narrative max), divided into:
  • Significance
  • Innovation
  • Approach

Specific Aims

This standalone page should define your Phase II goal and break it into 2–4 clearly stated aims. Each aim should be measurable and tied to a logical milestone (e.g., “demonstrate 95% accuracy in field validation,” “complete GMP manufacturing protocol,” etc.).

Use plain language. Briefly introduce the problem, your Phase I success, and how Phase II will build toward a product. End with a statement of impact—e.g., “Successful completion will result in a validated device ready for regulatory submission.”

Research Strategy

Break this into the required subheadings: Significance, Innovation, and Approach. Use formatting (bolded subheadings, paragraph breaks) to help reviewers skim and retain information.

• Significance:
  • Define the unmet need. What is the public health or research impact?
  • Explain how your solution addresses that need.
  • Cite market data or public health statistics where relevant.
  • Tie the project to commercial potential and NIH’s mission.
• Innovation:
  • Clarify what’s new: A novel mechanism? Platform? Application?
  • Compare briefly with existing solutions.
  • Mention IP status if applicable—provisional patents, trade secrets, etc.
  • Emphasize practical advantages: faster, cheaper, more scalable.
• Approach:
  • Organize by Specific Aims.
  • For each: describe the design, key tasks, data collection methods, success criteria.
  • Include controls, benchmarks, and statistical plans if applicable.
  • Address potential problems and contingency plans.
  • Reference Phase I results as preliminary data—use tables or figures if allowed.
  • If human subjects or animals are involved, briefly note how those will be handled (full details go in separate sections).

Integrate commercialization context. As this is an SBIR application, reviewers expect the R&D to move the product closer to market. In each aim, note how success contributes to commercialization—whether that’s scalability, validation, regulatory readiness, or user acceptability.

Support your case. Reference prior work, published benchmarks, and include citations. Strong letters of support from partners or advisors can help, especially if they show interest in using, licensing, or funding your product post-Phase II.

By the end of this section, reviewers should feel confident that your scientific plan is solid, your innovation is meaningful, and your team can deliver.

Write a Strong Commercialization Plan

Your Commercialization Plan is just as critical as your Research Strategy. NIH Phase II applications require a detailed 12-page Commercialization Plan—submitted as a separate PDF attachment. Reviewers want to see that your innovation isn’t just scientifically sound but commercially viable.

Use NIH’s six-section structure, and label each heading clearly:

1. Value Proposition and Expected Impact
   Start with what problem your product solves, and who needs it. Describe the potential market impact and public health benefit. Be specific—quantify outcomes where possible. Example: “Reduces hospital readmissions by 22%, saving an estimated $4.5M annually per system.”
2. Company Overview
   Summarize your business: mission, structure, founding year, key team members. Highlight relevant technical and business experience. If you have an advisory board, industry partner, or prior funding, include it here.
3. Market, Customer, and Competition
   Define your customer: hospitals, clinics, labs, pharma, consumers? Include estimated market size, growth rate, and buyer dynamics. Describe how customers currently address the problem—and why your solution is better. Acknowledge competitors and state your advantage (cost, performance, UX, etc.).
4. Intellectual Property
   List any patents filed, granted, or in preparation. Mention trade secrets or exclusive licenses. If applicable, note a Freedom to Operate (FTO) assessment. Strong IP signals to reviewers that your innovation can hold a market position.
5. Financing Strategy
   Explain how you’ll fund the product after Phase II. Will you seek venture capital? Strategic partnerships? Government procurement? Note any current investor interest. If pursuing Phase IIB or co-investment programs, mention that too.
6. Revenue and Production Model
   Describe how your company plans to make money: product sales, licensing, B2B deals, SaaS subscriptions, etc. Outline how you’ll produce and deliver the solution at scale. Include key partnerships (CMOs, distributors, etc.) if already in place.

Include your 12-page Commercialization Plan as a separate PDF attachment.
Omitting it is a common mistake—and will render your application incomplete.

Keep your tone business-focused. This isn’t the place for technical deep-dives—that’s for your Research Plan. Instead, focus on how your innovation becomes a sustainable, investable solution.

If available, attach Letters of Support from industry collaborators, investors, or potential customers. These can be powerful validators.