Regulatory Operations Best Practices for Health Canada Submissions

Health Canada accepts electronic Common Technical Document (eCTD) submissions for pre-clinical trial application consultation meetings, clinical trial applications (CTA), amendments, notifications, and responses for post-clearance data related to those applications. CTA submissions via eCTD were a significant step in the propagation of eCTD. The adoption of eCTD for CTAs stemmed from a successful pilot the health authority conducted. 

Like submissions before eCTD, Health Canada reviews the package and issues a no-objection letter (NOL) before a sponsor initiates a trial or an amendment to a trial. And the same process is applicable; pharmaceuticals go to the Therapeutic Products Directorate and biologics to the Biologic and Radiopharmaceutical Directorate. 

As part of Certara’s Drug Development Solutions, our Regulatory Operations team supports sponsors through the eCTD submission process. RegOps tracks all components of a CTA, publishes the components for CTA submissions in eCTD format, and validates each submission to ensure technical compliance. The submissions are prepared in our proprietary software platform, GlobalSubmit™, and can be easily viewed by sponsors in GlobalSubmit™ Review. 

Once a sponsor files in eCTD format, all subsequent transactions for the same submission must also be in eCTD format. Any regulatory submissions under 10 gigabytes must be electronically transmitted via the Common Electronic Submissions Gateway (CESG).  The CESG is where submissions are uploaded and reviewed by the health authority. This process is much faster compared to the days of mailing in a CD-ROM or other media. The CESG is synonymous with the FDA’s Electronic Submission Gateway (ESG), which was upgraded when the next-generation gateway (ESG NextGen) went live in April 2025. 

You can refer to the Health Canada Filing Submissions electronically page, where the following information is available: 

• Guidance on accepted electronic formats
• Organization and placement of documents for Canadian Module 1
• Validation rules for regulatory transactions in eCTD format 

There are still a few activities that are “out-of-scope” for filing in eCTD format, such as submitting clinical trial site information, adverse reaction reports, or applications for license of medical devices. 

Please see Health Canada’s website for details, including information and instructions on filing electronically. Their website also provides additional information on Health Canada and eCTD, including the option to submit CTAs via eCTD. 

As of January 1, 2020, all new Drug Master Files must be prepared in eCTD format. Plus, regulatory transactions for Master Files prepared in eCTD or the non-eCTD format must be sent via the Common Electronic Submission Gateway (CESG).  The CESG was modernized with the deployment of ESG NextGen in April 2025 to offer a more secure and efficient means of sending regulatory submissions. 

Previously, it was permissible to send Master File transactions on physical media, such as compact disc, DVD, or USB.  However, as of January 2020, this is no longer possible. Unless the contents and files are greater than 10 GB, the submission files must be sent via the CESG. 

If you need to submit clinical trial applications or master file submissions using eCTD format to Health Canada, we can help. Our Regulatory Operations team has expertise in eCTD submissions and CESG transmission to Health Canada.  Our expert submission support is further enhanced by our proprietary eCTD software for seamless integration of regulatory services and software. At Certara, our highly qualified professionals can help you achieve accelerated regulatory submission success. 

To learn more, read the below white paper.