Top 5 eCTD Submission Mistakes and How Our eCTD and Regulatory Publishing Services is at the forefront

Tom Marsden
Apr 26
3 min read

Submitting an electronic Common Technical Document (eCTD) to authorities like the FDA, EMA, or PMDA is a pivotal step in regulatory approval—and any mistake can cause costly delays.A single misstep can lead to technical rejections, review delays, or additional queries, all of which can derail your regulatory strategy and slow down your product's journey to market.

At eCTD Pharma, our expert eCTD publishing services and regulatory submission support are designed to eliminate these risks. With a global track record supporting pharmaceutical and biotech companies, we ensure every submission is fully validated, agency-compliant, and error-free.

Below, we reveal the top five most common eCTD submission mistakes—and how our services help you avoid them.

1. Incorrect Folder Structure or File Naming in eCTD Submissions

Strict adherence to the eCTD format is critical, including correct folder structures and file naming conventions based on ICH and region-specific standards.

Common Mistakes:

Misplacing documents (e.g., placing Module 3 content in Module 2)
Using forbidden characters or non-standard filenames
Ignoring regional specifications (like FDA’s Module 1 requirements)

Why It Matters:Submissions with incorrect structures are often automatically rejected during technical validation, causing costly delays and rework.

How eCTD Pharma Helps:

We use validated publishing platforms like GlobalSubmit™ to enforce ICH-compliant structures.
Our team ensures filenames meet FDA’s eCTD Technical Conformance Guide standards.
Every submission undergoes rigorous pre-validation to catch and correct errors before sending.

2. Non-Compliant PDF Formatting

PDFs form the core of every eCTD submission. Minor formatting issues can trigger major setbacks.

Common Mistakes:

Submitting PDFs that are not PDF/A compliant
Missing embedded fonts or searchable text
Poor-quality scans or missing bookmarks and hyperlinks

Why It Matters:Non-compliant PDFs can fail validation or frustrate reviewers, slowing the review process.

How eCTD Pharma Helps:

We ensure full PDF/A-1b compliance and optimize PDFs per FDA, EMA, and PMDA standards.
All documents have embedded fonts, 300 DPI resolution, searchable text, and proper bookmarks.
Our PDF optimization service ensures faster uploads and quicker reviewer navigation.

3. Incomplete or Incorrect Metadata in the eCTD XML Backbone

The XML backbone drives your eCTD’s organization. Any errors here can compromise the entire submission.

Common Mistakes:

Missing key metadata like application number or submission type
Using wrong lifecycle operations (e.g., wrong "replace" or "append" tags)
Submitting with outdated DTD versions

Why It Matters:Errors in metadata can cause agency systems to misinterpret your submission, risking rejection or additional reviewer queries.

How eCTD Pharma Helps:

We ensure full compliance with the correct Document Type Definition (DTD), whether eCTD v3.2.2 or eCTD v4.0.
Advanced XML validation tools aligned with agency schemas ensure flawless metadata.
Every submission undergoes extensive technical checks before final publishing.

4. Skipping Validation Before Submission

Rushing through or skipping validation is one of the most damaging mistakes.

Common Mistakes:

Not using agency-endorsed validation tools
Ignoring high-severity errors or warnings
Overlooking region-specific validation requirements

Why It Matters:Skipping validation leads to technical rejection—meaning wasted time, additional costs, and delayed approvals.

How eCTD Pharma Helps:

We validate every submission using FDA and EMA-approved tools like GlobalSubmit VALIDATE or Lorenz eValidator.
All critical and major errors are resolved prior to submission.
We adhere to the latest FDA eCTD Validation Criteria and EMA eCTD guidelines for every sequence.

5. Poor Lifecycle Management for eCTD Amendments and Variations

Managing the lifecycle across multiple sequences is critical for maintaining regulatory clarity and consistency.

Common Mistakes:

Improperly referencing prior sequences
Misusing lifecycle operators (like "new" instead of "replace")
Failing to maintain a clear and auditable submission history

Why It Matters:Poor lifecycle management can lead to agency confusion, submission rejection, or requests for clarification.

How eCTD Pharma Helps:

We maintain a comprehensive lifecycle management system tracking every sequence and reference.
Proper lifecycle operators are always used (e.g., "replace", "append"), preserving document history and integrity.
Our expert team handles lifecycle management for all submission types—INDs, NDAs, CTAs, MAAs, and beyond.

Why Choose eCTD Pharma for eCTD Services?

At eCTD Pharma, we combine cutting-edge technology, deep regulatory expertise, and global insight to deliver submission excellence.When you partner with us, you gain:

Validated eCTD publishing tools for global submissions (FDA, EMA, PMDA, and more)
Expert formatting, PDF optimization, and XML metadata management
Agency-specific compliance for faster approval times
Reduced post-submission queries and minimized risks of rejection

Our mission is to make your submission seamless, compliant, and successful.

Let's Talk About Your Next Submission

Avoid costly mistakes. Accelerate your regulatory success.Partner with eCTD Pharma for expert-led eCTD publishing and regulatory submission support.

Contact Us Today:Email: info@ectdpharma.com

Web: www.ectdpharma.com