Explain To Me – Beaker Charging – Pathology Billing

Happy New Year from the Honeydew Consulting Team! A new year means a new start with a new blog post, and we will kick the year off with Pathology Billing!

For those who have experience with Epic Beaker, you will know that being knowledgeable in Beaker requires extensive application and integrated knowledge to be successful. This is because the laboratory is not only integral in medical decision making, but also is specialized compared to other departments in many ways. One example of this is laboratory billing. Lab billing requires knowledge of laboratory-specific rules and regulations as well as the information required on all charges.

As such, it is paramount that Beaker consultants have a firm understanding of how lab billing works to best support their clients. Due to the extensive nature of this topic, we will be presenting this in several different articles throughout the near future.

What is Lab Billing?

Lab billing is very different from physician, facility or DME (durable medical equipment) billing specialties. It centers around a very specific set of CPT codes that includes services that are used to evaluate specimens.

At a high level, this can be broken up into two types of charges, technical and professional charges. Technical charges in the lab refers to any services that are performed either by a lab tech (such as a histotechnologist creating slides) or a lab instrument. Professional charges can be thought of as the services a pathologist will perform, such as interpreting pathology specimens.

Pathology Billing

Pathologists are board-certified physicians who specialize in diagnosing diseases through patient specimens. Hospital systems that have anatomic pathology labs will employ pathologists to perform interpretations of patient specimens such as biopsies, pap smears, or excisions.

The general process of a pathology case is as follows: The Anatomic Pathology (AP) lab receives specimens that have been collected in the operating room or in the clinic. These specimens need to be cut, processed, stained, and/or otherwise altered and placed upon a slide (or many slides). These slides are then provided to the pathologist who will interpret them and form a diagnosis. The pathologist may potentially order more tests/slides in order to form their diagnosis.

As the histotechnologists prep the specimens and build out a case within Beaker, charges are being generated in the background. Both specimen and task protocols can carry charges. Generally, an organization will set up specific specimen protocols that include one to many task protocols within it. Additionally, other task protocols can be added to the case individually as appropriate on a case-by-case basis. Once the case is passed on the pathologist for interpretation, additional charges may be generated and can be added to the case using automatic or manual processes.

It is important to note that not all pathologists are employed directly through a hospital, but are instead part of an outside pathology group. As such, different organizations will need to get a clear understanding of how their pathologists are paid in order to choose the best billing solutions to meet their needs.

In-House Pathologist Billing

Many organizations choose to employ pathologists directly rather than contracting with a pathology group. In-house pathology billing is subject to the same rules and regulations as third party billing. Unlike with third party billing, there is generally no need to worry about generating flat files or extracts when working with in-house pathologists because charges originate and are billed out of Epic.

At many organizations, pathologists are responsible for reviewing the charges on the case to ensure that they are correct prior to finalizing and signing out the case. Once the case is signed out, the charges are dropped and go through the charge router and through any internal billing rules and processes set up in Epic and will post to the patient’s hospital or professional account depending on if the charge is technical or professional.

Third Party Billing

When pathologists are part of a medical group, it means that they are not paid through the hospital they are working with, but instead paid through the pathology group of which they are a part. As such, it is important for them to receive all the necessary billing information from the lab in order to properly get paid for their services. Depending on the organization needs, the requirements can vary regarding how they want this data extracted.

The two most common approaches to providing Beaker anatomic pathology charges we see is sending out reports to a third party billing service, such as an APS (automated payment system), or by generating a flat file containing the necessary billing information.


Of the two approaches, providing a report to the third part billing service is generally the more simple route. It only requires the printing the report and sending it to said pathology group. This can be achieved by physically printing the report and physically mailing it out. Another option is to use result routing to print a .pdf file of the report to a specific electronic folder location, where an automated process takes up the files from that specific folder and delivers them to a SFTP (Secure File Transfer Protocol) owned by the third party billing entity.

Flat File

Sending a flat file is the more involved of the two approaches. This approach involves creating a billing extract to pull the desired information from within Epic. When creating the billing extract, you will need use the billing specifications of the third party billing entity; and you will need to work closely with the third party to ensure they are getting the correct information as well as all of the needed information to correctly bill. The difficult part here is that more often than not, the extract needs to be in a specific format. This format can include the size of the columns, location of items, and data formatting. As such, considerable testing will need to be performed to ensure that the extract is being generated in a format that can be easily consumed. Similar to the report option above, the extract is then sent to a specific folder location, from which it is SFTPed to the billing entity.

One thing to note is that unlike reports, you will need to work with the Professional Billing team to update charge router logic within Epic to identify the appropriate charges to send to the extract.

If you have any questions or are looking for additional help with Pathology Billing, reach out to us at [email protected].