The Secret to Billing Endoscopic Procedures

September 6th, 2022 - Chris Woolstenhulme
Categories:   Gastroenterology   Coding  

Billing endoscopic procedures can be confusing, but coding rules will assist in this process. Most of the coding principles we will review are the same as any other type of coding; however, endoscopic procedures are paid differently.  This article will address the process of how to find the correct code selections for endoscopic procedures and hopefully help your revenue cycle.     

"The gastroenterologist performs an upper GI EGD with multiple biopsies and botox injection."
Let's review this scenario; we found 43235, 43236, and 43236 that may apply. 

#1 It is a Family Thing
CMS Classifies endoscopic procedures by family and considers other related procedures in the same endoscopic family for payment. Since the procedures all correlate to a family, there is always a parent code, also called an "Endoscopic Base Code," the base code reflects the main procedure. For example, 43239 has a base code of 43235; notice the description below (Figure1.) 43235 is designated as a (separate procedure) and also referred to as the base code. If a code is defined as a separate procedure (parent code), it cannot be coded with other codes in the same family.

What is a parent code? 
The parent code includes the full description of the procedure up to the semicolon, and the indented code(s) beneath the parent code includes additional information on the procedure(s), indicating further work was done, all being in the same family.

We selected the esophagogastroduodenoscopy (EDG) family codes.

Figure 1. Code family and descriptions

Parent Code:
(Endoscopic Base Code)
43235 EDG - Esophagogastroduodenoscopy, flexible, transoral; diagnostic, including the collection of specimens(s) by brushing or washing, when performed (separate procedure)
Child Code 43239 EGD, with biopsy, single or multiple
Child Code 43236 EGD, with directed submucosal injection(s), any substance

Now we understand we cannot code the parent code with the other codes in the same family, but we have two child codes to consider; how do we know which one to use, and can we use a modifier on one? Good question. Let's dive a little further into our code selection.

#2 Understanding NCCI Code Pair Edits (identifying codes that can be reported together)
The National Correct Coding Initiative (NCCI) code edits are prepayment edits to prevent improper payment on bundled codes. If there is an NCCI edit, the tables will indicate the code pairs in either Column 1- as payable or Column 2 as not payable (unless a modifier is appropriate). 

In addition, each CPT code has an assigned Modifier Indicator to inform us whether or not a modifier is allowed to override the edit; see column 2 code section. Is there a Superscript 1 or Superscript 0 next to the Column 2 code? 

Figure 2. NCCI Column 1 and Column 2 code pairs

Generally, when a procedure is bundled into another procedure, the NCCI edits say they should not be reported together. For example, if a procedure is performed at different levels of complexity, the more extensive procedure includes the less complex procedure. However, there are exceptions, and endoscopic procedures are an exception to this rule, which will be covered later in this article.

Note: If a modifier is allowed, it will always be on the Column 2 code.  

Figure 3. Column 1 and 2 descriptions

Column 1 Payable
Column 2 not payable (unless a modifier is allowed)

#3 Selecting the Codes that Require a Modifier
We know the Column 2 code will have a modifier indicator next to the code that determines which codes are eligible for a modifier bypass (if any).

There are three modifier indicators "0", "1," and "9".

Figure 4. Modifier Indicators

Modifier Indicator

Description and Rationale

0 "There is no modifier allowed to bypass edit."
The two procedures/surgeries cannot be reported together if performed at the same anatomic site and same patient encounter. No modifier can be used to bypass this edit.
1 "A modifier may be allowed to bypass edit."
Indicates there may be an edit bypass with an appropriate modifier
9 "NCCI edit does not apply to code pair."
The NCCI edit does not apply to the code pair

To learn more about modifier indicators and the NCCI tools, see CMS and the Medicare Learning Network Medicare National Correct Coding Initiative (NCCI) tools. 

Notice the modifier indicator (see highlighted in Figure 2) when looking at 43239 in column 2 (432361). The code pair is not payable; however, the code pair edit may be overridden with a modifier (if appropriate and allowed), identified by a Superscript 1.

Tip: If the NCCI-associated modifier is not used, the column two code will be denied.  

There is still more to consider; we selected our codes using the NCCI edits. We need to determine how CMS pays these codes, which will help us understand pricing and payment on these codes. For more information on pricing and payment policy indicators, visit CMS, Medicare Fee Schedule Indicators (MPFS)  

What does Medicare say?

Endoscopies (multiple): Medicare has special payment rules for multiple endoscopies performed on the same day. Modifier 51 will be added, by Noridian, to reduce services if necessary. Providers should not append this modifier to any services. We will cover the rationale in more detail. 

Note: Keep in mind these are CMS rules; other payer rules may be different if they do not follow CMS rules. 

This information is related to the code scenario we are currently working on. When coding other endoscopic procedures, be sure to verify the MPFS Indicator list for endoscopic base codes
for more information on related/unrelated endoscopies and same-day procedures.

#4 Medicare Fee Schedule Indicators (payment policy)
Understanding Medicare Physician Fee schedule (MPFS) Indicators are one of the most overlooked aspects of coding and yet offers essential information on how CPT codes are processed and paid. Medicare is not the only payer using the MPFS indicators. Medicare sets the standards for other payers as well; many commercial payers follow Medicare's rules, so it is essential to understand the use of MPFS indicators. The payment policy indicators also give information such as global surgery days, multiple surgery indicators, and the applicability of professional and technical components.

Don't overlook this vital part of coding!

Since we are looking at reporting multiple procedures, in this article, we will review just the multiple procedure indicators. 

Multiple Procedure Indicators
The multiple procedure indicators identify which payment adjustment rule for multiple procedures applies to the service.

According to CMS, endoscopies are subject to the multiple endoscopy reduction and can be identified with an indicator of "3" in the multiple procedure field on the CMS PFS RVU File. The reduction occurs when an endoscopic procedure is reported with another endoscopic procedure in the same base endoscopy family.

CMS has categorized endoscopic procedures 43239 and 43236 with the multiple indicator "3"; this tells us CMS will apply multiple reductions on additional procedures with the same base procedure. See the complete description below. 

43239 and 43236  Multiple Procedures (51): 3
Special rules for multiple endoscopic procedures apply if the procedure is reported with another endoscopy in the same family (i.e., another endoscopy having the same base procedure). The base procedure for each code with this indicator is identified in the endobase field of this file. Apply the multiple endoscopy rules to a family before ranking the family with the other procedures performed on the same day (for example, if multiple endoscopies in the same family are reported on the same day as endoscopies in another family or on the same day as a non-endoscopic procedure). If an endoscopic procedure is reported with only its base procedure, do not pay separately for the base procedure. Payment for the base procedure is included in the payment for the other endoscopy.

43235- (Parent Code) Multiple Procedures (51): 2
Standard payment adjustment rules for multiple procedures apply. If the procedure is reported on the same day as another procedure with an indicator of 1, 2, or 3, rank the procedures by fee schedule amount and apply the appropriate reduction to this code (100%, 50%, 50%, 50%, 50% and by report). Base the payment on the lower of (a) the actual charge or (b) the fee schedule amount reduced by the appropriate percentage.

Tip:  NCCI Edits Validator considers all of the code pair edits we have learned about so far and others we have not discussed in this article. 

NCCI Coding Policy Manual: 
C. Endoscopic Services 2. If multiple endoscopic services are performed, the most comprehensive code describing the service(s) rendered shall be reported. If multiple services are performed and not adequately described by a single HCPCS/CPT code, more than one code may be reported. The
multiple procedure modifier 51 should be appended to the secondary HCPCS/CPT code. Only
medically necessary services may be reported. Incidental examination of other areas shall not be
reported separately.

#5 Payment for Same Family - Selecting Code Order
Medicare payers will reimburse the highest valued procedure at 100% of the allowed reimbursement, and any additional procedures done during the endoscopic procedure in the same family will be reimbursed at 50%. 

CMS will automatically process claims by paying for the most costly procedure; DO NOT append modifier 51 to CMS claims. Other payers may pay according to how you code the claim or require something different, be sure you understand your payer guidelines. 

Remember: CMS will not pay for the base procedure twice.

#6 Choosing the Correct Modifier
Payer guidelines will determine the modifier; it is essential to note that every payer may not require the same modifiers. Consult your payer to determine if modifier 59 is required; some payers may require reporting 59 and 51 modifiers. Use Modifier 59 when a procedure is at a separate location and allowed with GI procedures. Modifiers are either informational or functional. Since the functional modifiers affect reimbursement, report functional modifiers for an endoscopy on the codes from highest to lowest RVUs or allowable amounts. Even if CMS has eternal edits allowing payment for the most costly procedure, it is good practice to code them accordingly.  

NOTE: The modifier will not always be required in this order; it will depend on the procedure and the reason for the procedure. 

                                                       Putting it all Together

#1 It is a Family Thing
Verify the correct codes, parent codes, and which child codes can be reported. 

43239 and 43236 should both be considered, not the parent code. 

#2 Understanding NCCI Code Pair Edits (which codes can be reported together)
NCCI Code Editor: Check the Column I and Colum 2 codes.

*43236 is a Column 2 code – Indicating it can be used with a column 1 code. 

#3 Selecting the codes that Require a Modifier
Modifier indicators determine if your code(s) can use a modifier to bypass the edit, using the modifier Indicator, 0, 1, or 9. 

43236 has a #1 modifier indicator. "A modifier may be allowed to bypass edit"

#4 Medicare Fee Schedule Indicators
Multiple endoscopies are subject to the multiple endoscopy reduction rules and can be identified with an indicator of "3" in the multiple procedures. 1, 2, or 3, rank the procedures by fee schedule amount reduction to the code (100%, 50%, 50%, 50%, 50%, and by report).

* 43236 and 43239 CPT codes both have a multiple procedure reduction of "3", indicating the first reported CPT code will be paid at 100%, and the 2nd CPT code and beyond will be paid at 50%.  

#5 Payment for Same Family - Selecting Code Order
Medicare payers will reimburse the highest valued procedure at 100% of the allowed reimbursement, and any additional procedures done during the endoscopic procedure in the same family will be reimbursed at 50%. Due to this, the higher-cost procedure would be the first CPT code line item.

43236              $400.02  (higher cost procedure- Done in office)
43239              $375.45  (lower cost procedure- Done in office) 

#6 Choosing the Correct Modifier
The modifier may be payer-specific. Modifiers are either informational or functional, and functional modifiers affect reimbursement.  Be sure to report functional modifiers for an endoscopy on the codes in order from highest to lowest RVUs or allowable amounts. Remember CMS does not require the 51 modifiers; other payers may.  

43236 X1
43239 X1 Modifier 51 

Where to Find this Information 
Public files are available on; you be sure to download the most current data file and watch for updates throughout the year. Or for a more simple solution is to use Find-A-Code. This information and much more can be found on each code information page.

                                   Using Find-A-Code to Determine Fee Schedule Indicators. 

Each CPT code page has the following information under the "Additional Code Information (global Days, MUEs, etc.) tab.

Figure 5. Additional code information

You can also find the File on, be sure to download the current file. This file shows the Multiple Procedure indicators for each code and the Endo Base Code (Note: keep an eye out for file updates to ensure you are on the most current release). 

Figure 6. CMS Data File Example

Take the time to review your payer's policies and clearly understand modifier usage, medical records review, placement of CPT codes and modifiers in their correct positions. For example, if bleeding occurred during the EGD, you would not apply a modifier 59; however, if the bleeding was present and the procedure performed was due to bleeding, Modifier 59 may be applicable. 

This article Is informational only and not based on legal service or advice; every coder is expected to do their research according to specific findings. This information is to be used only as guidance in coding.    

If you found this information helpful, or have a suggestion for an article, let us know by contacting us at 

Other resources:
IOM, Publication 100-04, Medicare Processing Manual, Chapter 12, Section 40.6C.13. 30.1 - Digestive System (Codes 40000 - 49999) 


Questions, comments?

If you have questions or comments about this article please contact us.  Comments that provide additional related information may be added here by our Editors.

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