CollaborateMD FAQs

General

• When Electronic Statements are turned on in CMD, patients without an email address tied to their profile will receive a paper statement instead. If a patient prefers not to get electronic statements, make sure that there’s no email address entered in their profile. The system will automatically send paper statements to those patients.

  Check out this CMD article for more information on Electronic Statements.

• When patient information is transmitted, CollaborateMD attempts to match the incoming data to an existing active patient account.

  If the original patient account is inactive, the system does not match it. As a result, CollaborateMD does not recognize the original record and creates a new patient account instead.

  This behavior can be confirmed in the Interface Tracker, where the following messages appear:

  

  • WARNING – Unable to find existing patient with Account: 68463010
    This message means the system searched for an active patient account using the provided account number, but did not find one. Inactive accounts are excluded from the matching process.
  • INFO – Created new patient: XXXXXX, XXXXXXXXX (68463039)
    This message confirms that, because no active patient record was found, the system created a new patient account. This newly created account is a duplicate.

  These messages help explain why the duplicate was generated and confirm that the original account was inactive at the time of transmission.

  • For detailed instructions on merging duplicate patient accounts, refer to the CollaborateMD help article on merging a patient account.
  • For more information, see checking for duplicate patients.

Payer Agreements

• A payer agreement is a legal form that outlines the electronic transactions that will occur between an insurance payer and the practice or provider.

• Payer agreements establish the required electronic connection between your billing system and the insurance payer. They enable your organization to:

  • Submit electronic claims (EDI 837 files): Without an approved payer agreement, claims cannot be transmitted electronically to the payer.
  • Receive Electronic Remittance Advices (ERA/EDI 835 files): Payer agreements authorize the payer to send remittance information back to your system so payments can be posted electronically.

  In short, payer agreements ensure both outbound electronic claim submission and inbound ERA posting function correctly.

• Payer enrollment should be completed by the facility. It may be completed by an Account Admin or any user with Payer Agreement permissions.

• Payer agreements are completed at the Tax ID level.

  • If you bill using multiple Tax IDs for a provider, each Tax ID requires its own payer agreement.
  • If you only bill under one Tax ID, only one agreement is required.

  However, requirements vary by payer and state. Some payers may require an agreement for each NPI, even if they share a Tax ID. We recommend contacting your payer directly to confirm their specific requirements.

• A new agreement is typically required when changes occur on the payer's side, such as updates to the Payer ID or payer connections. Additionally, if your Tax ID or NPI has changed with the payer, a new agreement may be required. Providers should confirm directly with the payer whether updated enrollments are needed after any change.
• CollaborateMD's system does not track or display who physically completed the payer agreement. It only records the authorized signer associated with the agreement. Because of this, users cannot verify which individual submitted the agreement, only who formally signed and approved it.
• If the Authorized Signer information is needed, contact Integrated Billing Support at [e-mail] and provide the customer's name and payer information related to the agreement.

Claims

• The diagnosis codes sent via HL7 messages are determined and organized using the following logic:

  • Primary Diagnosis/Principal: Always sent in position 1 of the diagnosis code list.
  • Additional Diagnoses/Other: Sent in positions 2–18.
  • Admitting Diagnosis: Always sent in position 19.

  The order (1–35) in which the codes are sent in the HL7 message directly corresponds to where they are mapped—for example, position 1 will always populate the Primary Diagnosis, and positions 2–18 will populate the Additional Diagnoses section.

  • To download your batch, please reference the following link: Download Batch.
  • To view messages in the CMD Interface Tracker, please reference: Retrieve Interface Messages.

  Note: Diagnosis codes can only be sent 18 at a time. If your patient has more than 18 diagnosis codes, only the first 18 will be sent.

• We recommend creating a new authorization in the following circumstances 

  • When the patient receives a new authorization with a new authorization number. 
  • When a new Level of Care is being authorized.
  • When the existing Level of Care is extended with a new authorization number.
  • When the patient transitions from one Level of Care to another, e.g., Residential to Detox.

  For more detailed instructions and information on utilization reviews, users can refer to this article.

• If you get the error message, “Sorry, an unexpected error prevented the data center from completing. The clearinghouse may be experiencing a service interruption,” it means that the clearinghouse is experiencing a temporary service interruption. During this time, real-time submissions cannot be processed, so affected claims are automatically queued for nightly batch submission instead.

  If submitting the claim later doesn't work, no additional action is required. The claim will be automatically sent during the nightly batch process at 11 PM EST. If the claim does not transmit after the nightly batch, contact IB Support. 

• You may encounter difficulty when attempting to send corrected (replacement) or voided claims to Medicare or Medicare Advantage payers in CollaborateMD because they do not allow corrected or voided claims or require certain frequency codes.

  Medicare

  Medicare does not accept corrected (replacement) or voided claims via electronic submission (837 format). If a previously submitted claim was incorrect or requires changes, CollaborateMD recommends:

  • Resubmitting the claim as an original claim (frequency code = 1).
  • Ensuring that all corrections are made before resubmission.

  Otherwise, the payer will identify the claim as a duplicate and process it accordingly, potentially denying or reprocessing based on their matching logic and internal policies.

  Medicare Advantage Plans

  Most Medicare Advantage plans do allow corrected and voided claims. In CollaborateMD, this is done by submitting claims with:

  • Frequency Code 7: Replacement of Prior Claim
  • Frequency Code 8: Void/Cancel Prior Claim

  These claims should reference the original claim number (ICN) to be accepted and processed properly.

  For more information, check out these articles:

  • Re-submit a Claim
  • How To Resubmit Rejected Claims

• When Hard Close is enabled, and a claim is submitted with a date of service before the Hard Close date, the claim won’t be created in CollaborateMD. Instead, the system will show an error in the Interface Tracker. This behavior helps prevent claims from being sent with dates of service that are outside the allowed posting period.

  Check out this article for more Hard Month Close FAQs.

• While the EMR will not allow the same NPI to be used for more than one user in the managed user's list of profiles, the system will auto-generate 9999999999 in the place of a user's NPI if the NPI is missing from the user's profile when applying Clinical Provider workflows for Integrated Billing. Click here for more information about clinical billing providers and Box 19.

• Currently, there is no automation available in CollaborateMD to change CPT codes when claims are forwarded to a secondary payer.

  1. If the secondary payer denies the claim due to an incorrect CPT code, manually update the CPT code on the denied claim. 
  2. Resubmit the corrected claim to the secondary payer.

  If automated CPT code updates would improve your workflow, you may submit a feature request through CMD’s Idea Exchange so their Development team can review it for potential future enhancements.

Reporting

• You can use the CollaborateMD Web API Service to run CMD reports without logging in. For more information, check the CollaborateMD Web API Services documentation.

• For single-customer reporting, the output is provided as a CSV file. If you’re working with the multi-customer endpoint, the output will be a ZIP file containing multiple CSV files.

  When the report runs successfully and returns results, the data is provided as a raw byte array of base64-encoded data. To access and use the results:

  1. Decode the data.
  2. Save or interpret it as a .zip file to extract the results.

  For additional details, please refer to the API Guide, specifically pages 19–22.

CLIA Number

When previewing claims in CMD, you may see your facility's CLIA number appear alongside the authorization number. This behavior is expected.

• The additional number you are seeing is the facility's CLIA number. CMD automatically populates the CLIA number on claims whenever an authorization number is entered.

• A CLIA number is a 10‑digit universal identifier assigned by the Centers for Medicare & Medicaid Services (CMS) to certify a laboratory or facility location. It verifies that the facility is authorized to perform specific laboratory services.

• This behavior is the result of updated system logic in CMD. When an authorization number is present, the system automatically includes the facility's CLIA number on the claim to support compliance with laboratory billing requirements. No manual entry is required.

• The CLIA number is pulled directly from the facility record in CMD. You can locate it by opening the facility associated with the claim and scrolling down to the CLIA number field in the facility's details.

• CLIA numbers are not payer‑specific. They are a universal identifier assigned to a facility and apply across all payers. However, some payers may specifically require a CLIA number in order to process or pay certain laboratory services.

• Payers use the CLIA number to:

  • Verify the facility's certification status
  • Confirm eligibility to perform billed laboratory services
  • Ensure compliance with federal billing requirements

  A valid CLIA number is required on claims (such as Box 23 on the CMS‑1500) for laboratory services to be eligible for payment.

• No. The CLIA number remains the same across all claims, regardless of whether the payer is Medicare, Medicaid, or a commercial insurance provider. Individual payers may have specific coverage rules tied to the certification level associated with that CLIA number.