Standard Operating Procedures for CLIA Compliance

As a laboratory partner and compliance-centric organization, Ovation helps startup labs or labs new to the molecular space understand CLIA compliance. Each lab workflow and standard operating procedure in your lab must be documented to meet CLIA regulations.  That’s why we created a full eBook to help labs like yours build SOP templates and lab manuals that are based on decades of CLIA experience.


As a laboratory partner and compliance-centric organization, Ovation helps startup labs or labs new to the molecular space understand CLIA compliance. Each lab workflow and standard operating procedure in your lab must be documented to meet CLIA regulations.  That’s why we created a full eBook to help labs like yours build SOP templates and lab manuals that are based on decades of CLIA experience. You’ll get an introduction into what CLIA is, who it impacts, and how to navigate the process of CLIA accreditation. Let’s dive in.

DISCLAIMER: These recommendations and template standard operating procedures are intended to be used for general purposes only. You should not rely upon the information in this eBook as a basis for making business, legal, or any other decisions. While we endeavor to provide the most accurate and updated information, makes no representations or warranties of any kind, express or implied about the completeness, accuracy, reliability, suitability, or availability with respect to this eBook for any purpose. This is not an all-encompassing guide to CLIA compliance. Any reliance you place on such material is therefore strictly at your own risk.

What should a molecular diagnostics laboratory SOP include to be CLIA- compliant?

Every lab needs to understand CLIA compliance. And this is especially true for startup labs as they look to grow into the diagnostic industry. Tenured former Laboratory Director and Ovation laboratory expert, Pauline Ghee, has compiled an extensive outline of exactly what you’ll need to get your lab on the road to CLIA certification and laboratory best practices. Achieving CLIA accreditation ensures quality testing standards and expands the complexity of testing your lab can process. Your commitment to these standards accelerates the creation of new therapies for infectious diseases and rare genetic disorders. Ovation is proud to partner with labs like yours to make more specific treatments accessible for patients in need.

Which labs need CLIA certification?

Before the Clinical Laboratory Improvement Amendments of 1988 or CLIA, testing was limited to independent hospitals and laboratories. Additionally, the complexity of tests and laboratories in which tests were performed was not considered. Now, CLIA has improved the standardization of laboratory testing and determined which laboratories have the capacity and ability to process certain test types. 

According to the CDC, The only laboratories NOT subject to CLIA standards are those that fall under the “waived tests” category. This CLIA-determined category includes simple tests with minimal chance of error or risk. These laboratories are exempt so long as they continue to perform testing in strict compliance with manufacturers’ instructions and regulations.*

How do I create a lab manual or lab standard operating procedure (SOP) to fulfill CLIA compliance?

Before diving into the steps to creating CLIA-compliant lab manuals or SOPs, you need to consider a few things.

  • Understand which type of CLIA certification your lab will need.
    • Certificate of Waiver: issued to a laboratory to perform only waived test.
    • Certificate for Provider-Performed Microscopy Procedures (PPMP): issued to a laboratory in which a physician, mid-level practitioner, or dentist performs no tests other than the microscopy procedures. Additionally, this certificate permits the laboratory to also perform waived tests.
    • Certificate of Registration: issued to a laboratory that enables the entity to conduct moderate or high complexity laboratory testing or both until the entity is determined by a survey to be in compliance with the CLIA regulations.
    • Certificate of Compliance: issued to a laboratory after an inspection that finds the laboratory to be in compliance with all applicable CLIA requirements.
    • Certificate of Accreditation: issued to a laboratory on the basis of the laboratory’s accreditation by an accreditation organization approved by CMS.
  • Ensure you are up-to-date on local and state regulations as they may include additional steps.
  • Ensure that all personnel are qualified by CLIA regulations for the duties they will perform on the outlined SOPNow that you’ve determined your specific certification type and laboratory staff requirements, you’re ready to start building your lab SOPs.

What are the foundational policies and procedures for CLIA compliance?

Begin your SOP documentation by understanding the standards for every person that will interact with a sample. These team members are responsible for upholding CLIA standards, and as such, must have the proper credentials and certifications required to maintain a high level of quality and accuracy in testing.

Compliant with the General Laboratory Systems 42 CFR § 493.1230 and other associated sections. 

    • ERGONOMIC POLICY: Personnel must have ergonomic work conditions, adjustable height of lab stools, minimization of repetitive motions required, etc.
        • Copies of credentials of testing personnel from Accessioning to QC and release of results to patients include
          • Copy of certifications (Board or otherwise), Degrees, Diplomas, and other professional certifications by ASCP
          • Copy of transcripts that verify the credentials listed in 1.b.1.i
          • Awards and other achievements
          • Job descriptions that succinctly outline authorizations, immediate reporting supervisor and subordinates, and responsibilities
          • Documentation of all Training listed in below

How do you properly train personnel for CLIA compliance?

Based on the complexity of your lab’s sample testing your personnel will need specific training on the operational workflows. To start, your staff should have a lab SOP that meets each of the following standards. 

  • Training of personnel SOPs
    • Training records for testing protocols
    • Competency Assessments on the exact protocols used for testing patient specimens
    • Safety training for handling infectious agents in accordance with CDC protocols
    • Safety training to meet OSHA requirements including how to handle spills, etc.
    • Training of HIPAA and IT security
    • On-boarding and training on the LIMS platform

This is only the beginning of the steps you need to take to prepare for CLIA-compliant workflows. To read the remaining SOPs and documents your lab needs to achieve CLIA compliance, you can download the full “Standard Operating Procedures for CLIA Compliance” eBook here.

How do you ensure the quality and safety standards in your lab meet CLIA standards?

CLIA-compliant labs know that they must adhere to specific quality assurance and validation studies standards to maintain accreditation. Not only do these additional steps maintain lab compliance, but they can also minimize room for human error—vital for laboratory success and building trust with providers. Before you prepare for applying for your CLIA certificate or accreditation, your team should have the following policies in place.  

  • QUALITY POLICY:  Preventative maintenance and calibration of instrumentation
    • Installation Quality/Operational Quality
    • Daily, Weekly, Monthly, Semi-Annually, Annually for each instrument including pipettors
    • Reconcile with manufacturers’ specifications, if operating outside of manufacturer’s ranges, validation studies must be performed to extend ranges to show that there is no decrement of performance
  • QUALITY POLICY:  Instrument calibration of all instruments for equivalency in performance every 6 months with a low, moderate, and high copy number of all channels used for detection
  • SAFETY POLICY:  Chemical and reagent inventory and chemical hygiene
    • Weekly safety walkthroughs documented
    • Emergency drills – evacuation, meeting points, communication policies, etc.
    • Emergency incidents or any harm to personnel

Additionally, we recommend your team create specific security and access policies. You can read more about those policies in the full version of this eBook, here.

What does CLIA look for in laboratory validation studies?

According to CLIA guidelines “The Technical Consultant/Technical Supervisor or Laboratory Director are responsible for ensuring the procedure used for verifying the performance specifications is adequate, as well as evaluating the results generated during the verification process.” 

To note, it is imperative that your lab compares the performance of the test system in your laboratory with the standards established by CLIA, as well as the manufacturer. This includes the following performance characteristics:

  • Accuracy
  • Precision
  • Reportable range
  • Reference intervals/range (normal values) for the laboratory’s patient population

You’ll need to create the following validation studies to prove consistent results and achieve CLIA accreditation. Remember, the more complex your tests are, the more stringent the validation studies required by CLIA become.

    • Optimizing your assay/test 
    • Determining the Limit of Detection (LOD
  • An appendix that organizes the raw data from all validation studies

As you continue to prepare your laboratory and laboratory staff for meeting CLIA standards and achieving accreditation, you can use the following list to ensure success under the scrutiny of a CDPHE onsite inspection/survey. Please note that this list does not include forms, logs, and work records that result from the execution of these SOPs and Policies but are required. In some cases, no reorganization or revision is needed. The set of SOPs for manufacturing the kit requires little editorial work.

What’s the difference between pre-analytic, analytic, and post-analytic phases?   

  • The pre-analytic testing phase occurs first and may include specimen handling issues that occur even before the time the specimen is received by the lab. But because errors with specimen handling and identification can occur in this phase, lab staff must be diligent to avoid allowing errors to funnel into the lab process.
  • The second phase is the analytic phase. This includes the diagnostic procedures, processes, and products that ultimately provide final results.
  • Finally, the post-analytic phase is last and leads to the production of a final result, value, or in histology, a diagnostic pathology report.

As you create lab training and procedures, be sure to keep each distinct phase in mind. We’ve separated them to ensure each piece receives the individual attention needed for CLIA compliance. 

Standard Operating Procedures organized according to CLIA requirements:

We’ve laid out the beginning of the SOPs that your lab will need in order of their CLIA requirements. Begin your documentation work with pre-analytic systems.

  • 42 CFR § 493.1240 – 1241; 1242 and other associated sections:  Pre-analytic Systems require the following organization to parallel the specimen journey. SOPs include:
    • Manufacture of specimen kits/tubes for collection
    • Specimen Collection of Saliva TwoStep:
    • Instructions and training of personnel at the point of collection
    • Accessioning operations to initiate Chain of Custody and procedures for checking specimen integrity, specimen type, and completeness of patient demographics in test requisitions and for communication of specimen rejection to allow for timely recollection.
    • QUALITY POLICY: Only specimens that pass Specimen acceptance should go through to the Analytic processing:
    • SOP: Instructions for use of the LIMS

After completing the previous steps, there are additional SOPs and policies required for the analytic, and post-analytic phases. Be sure to download the full “Standard Operating Procedures for CLIA Compliance” eBook to complete your SOP documentation journey. And if you have questions, reach out to for help furthering your lab’s growth with a LIMS.

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