Best Gastroenterology Billing Software 2026
Complete guide to GI practice billing solutions. Compare specialty-specific software with endoscopy integration, colonoscopy coding, and revenue cycle management for gastroenterology practices.
Key Takeaways
- ModMed gGastro is the leading GI-specific solution with integrated endoscopy documentation
- GI billing software costs $400-800/provider/month for integrated EHR + billing
- Endoscopy reporting integration is critical for accurate colonoscopy coding
- Quality metrics (ADR, cecal rate) should be tracked automatically for MIPS reporting
Gastroenterology practices face unique billing challenges. Complex endoscopy coding, multiple procedures per visit, quality measure tracking, and ASC vs. hospital billing require specialized software solutions that general medical billing platforms often can't handle efficiently.
This guide compares the top gastroenterology billing software options for 2026, covering features, pricing, and recommendations for different practice sizes. We'll also cover essential CPT codes, modifier usage, and quality metrics that impact your revenue and compliance.
Why GI-Specific Billing Software?
General practice management software often fails GI practices for several reasons:
General Software Limitations
- • No endoscopy report integration
- • Manual colonoscopy code selection
- • Limited polyp documentation
- • No ADR tracking
- • Poor modifier logic for multiple procedures
GI-Specific Advantages
- • Auto-populated codes from procedure findings
- • Polyp location/size to CPT mapping
- • Built-in quality metrics dashboard
- • Correct modifier sequencing
- • ASC/HOPD fee schedule awareness
Revenue Impact
GI practices using specialty-specific billing software report 8-15% higher collections compared to general solutions, primarily from proper modifier usage and reduced coding errors on complex endoscopy cases.
Top GI Billing Software Solutions
ModMed gGastro
Top PickGI-Specific EHR + Billing + Procedure Documentation
ModMed gGastro (formerly gMed) is the market leader for gastroenterology practices. It offers a fully integrated EHR, practice management, and billing solution designed specifically for GI with endoscopy documentation built-in.
Key Features
- • Integrated endoscopy reporting
- • Auto-coded colonoscopy findings
- • Quality metrics dashboard (ADR, cecal)
- • Patient portal & online scheduling
- • Integrated fax and patient messaging
- • MIPS reporting automation
Pricing (2026)
- • EHR + PM: ~$500-700/provider/month
- • RCM Services: 4-7% of collections
- • Implementation: $2,000-5,000
- • Custom pricing for large groups
NextGen Healthcare
Enterprise EHR with GI Specialty Templates
NextGen offers robust specialty content for gastroenterology including procedure documentation, GI-specific templates, and integration with endoscopy reporting systems like Provation.
Key Features
- • GI specialty content library
- • Provation integration
- • Advanced analytics
- • Population health tools
- • Multi-location support
Pricing
- • EHR + PM: ~$400-600/provider/month
- • Enterprise pricing for 10+ providers
- • Implementation varies by scope
Athenahealth
Cloud EHR with Strong RCM Services
Athenahealth offers a cloud-based EHR with excellent revenue cycle management services. While not GI-specific, its RCM team handles specialty coding and can integrate with endoscopy documentation systems.
Key Features
- • Rules-based claim scrubbing
- • Automatic claim status updates
- • Patient payment portal
- • Telehealth integration
- • Strong denial management
Pricing
- • Model: % of collections (4-8%)
- • No large upfront costs
- • Aligned incentives with practice
PrognoCIS
Affordable EHR with GI Templates
PrognoCIS offers a cost-effective EHR solution with specialty-specific templates for gastroenterology. Good option for smaller practices with tighter budgets.
Key Features
- • GI-specific templates
- • Integrated billing module
- • Patient portal
- • E-prescribing
Pricing
- • EHR + PM: ~$250-400/provider/month
- • Lower implementation costs
- • Good value for small practices
Provation MD
Endoscopy Procedure Documentation Specialist
Provation MD specializes in endoscopy procedure documentation with automatic CPT/ICD-10 coding. Typically used alongside a general EHR/billing system for the procedure documentation component.
Key Features
- • Structured procedure documentation
- • Auto-generated CPT codes
- • Quality metrics (ADR, etc.)
- • Image integration
- • Pathology tracking
Integration
- • Works with most EHRs
- • HL7 interface to billing
- • Often paired with Epic, NextGen
Essential Features for GI Practices
Endoscopy Documentation
- ✓ Structured procedure reports
- ✓ Polyp size/location capture
- ✓ Image integration
- ✓ Pathology result tracking
- ✓ Surveillance interval recommendations
Automated Coding
- ✓ CPT code suggestions from findings
- ✓ Modifier logic (-59, -XE, -22)
- ✓ ICD-10 mapping
- ✓ Multiple procedure sequencing
- ✓ ASC vs HOPD fee awareness
Quality Metrics
- ✓ Adenoma detection rate (ADR)
- ✓ Cecal intubation rate
- ✓ Bowel prep adequacy
- ✓ Withdrawal time tracking
- ✓ MIPS measure reporting
Revenue Cycle
- ✓ Eligibility verification
- ✓ Prior authorization tracking
- ✓ Claim scrubbing
- ✓ Denial management
- ✓ Patient statement generation
Critical GI CPT Codes for Billing
Colonoscopy Codes (45378-45398)
| CPT Code | Description | ~RVU |
|---|---|---|
| 45378 | Diagnostic colonoscopy | 5.84 |
| 45380 | Colonoscopy with biopsy | 7.24 |
| 45384 | Colonoscopy with hot biopsy/ablation | 8.13 |
| 45385 | Colonoscopy with snare polypectomy | 9.89 |
| 45388 | Colonoscopy with ablation of tumor | 10.31 |
| 45390 | Colonoscopy with EMR | 11.92 |
EGD Codes (43235-43259)
| CPT Code | Description | ~RVU |
|---|---|---|
| 43235 | Diagnostic EGD | 4.43 |
| 43239 | EGD with biopsy | 5.24 |
| 43251 | EGD with polypectomy | 6.37 |
| 43255 | EGD with hemostasis | 8.15 |
Critical Modifier Usage
- -59 (Distinct Procedural Service): Use when performing multiple different procedures (e.g., biopsy and polypectomy at different sites)
- -XE (Separate Encounter): Preferred over -59 when procedures occur at different sessions
- -22 (Increased Complexity): Document extensively for difficult polypectomies or unusual findings
- -52 (Reduced Services): Incomplete colonoscopy (failed to reach cecum)
- -53 (Discontinued): Procedure terminated due to patient condition
Endoscopy Reporting Integration
The connection between your endoscopy documentation and billing system is critical. Here's how the workflow should function:
Ideal Documentation-to-Billing Flow
Procedure Performed
Findings documented in real-time
CPT Codes Generated
Auto-populated from findings
Claim Created
Sent to billing for review
Claim Submitted
Electronic submission
Integration Best Practices
- • Ensure bi-directional data flow between procedure documentation and billing
- • Pathology results should auto-update ICD-10 codes when finalized
- • Quality metrics should populate without manual data entry
- • Images should be accessible from both systems
Quality Metrics & MIPS Reporting
Adenoma Detection Rate (ADR)
The percentage of screening colonoscopies where at least one adenoma is detected.
Target: ≥25% overall (≥30% men, ≥20% women)
Cecal Intubation Rate
Percentage of colonoscopies reaching the cecum with photo documentation.
Target: ≥95% of all colonoscopies
Bowel Prep Adequacy
Percentage with adequate preparation allowing complete examination.
Target: ≥85% with adequate or better prep
Withdrawal Time
Mean withdrawal time for negative screening colonoscopies.
Target: ≥6 minutes average
MIPS 2026 GI Quality Measures
GI practices should report these relevant MIPS quality measures:
- • MIPS 185: Colonoscopy interval for high-risk patients
- • MIPS 320: Appropriate follow-up interval for colonoscopy
- • MIPS 343: Screening colonoscopy adenoma detection rate
- • MIPS 130: Documentation of current medications
Pricing Comparison
| Solution | Monthly Cost | Implementation | Best For |
|---|---|---|---|
| ModMed gGastro | $500-700/provider | $2,000-5,000 | Mid to large GI practices |
| NextGen Healthcare | $400-600/provider | Varies | Multi-specialty groups |
| Athenahealth | 4-8% of collections | Minimal | RCM-focused practices |
| PrognoCIS | $250-400/provider | $1,000-3,000 | Small budget-conscious practices |
| Provation MD | $200-400/provider | $1,000-2,000 | Procedure documentation add-on |
Implementation Tips
1. Plan for Parallel Running
Run your old and new systems simultaneously for 2-4 weeks. This ensures no claims are lost during the transition and allows staff to build confidence with the new system.
2. Map Your Current Workflows
Document exactly how procedures flow from scheduling through final payment today. This helps identify gaps in the new system and ensures no steps are missed.
3. Train Billing Staff on GI Coding
Even with automated coding, billing staff need to understand GI-specific rules. Invest in AAPC or AHIMA training for colonoscopy and endoscopy coding.
4. Establish Quality Metric Baselines
Know your current ADR, cecal rate, and other metrics before switching. This allows you to verify the new system is accurately tracking these measures.
Frequently Asked Questions
What is the best billing software for gastroenterology practices?
ModMed gGastro is widely considered the best GI-specific billing software, offering integrated EHR, procedure documentation, and billing optimized for endoscopy centers. NextGen Healthcare and Athenahealth are strong alternatives for multi-specialty groups.
How much does gastroenterology billing software cost?
GI billing software typically costs $400-800 per provider per month for full EHR + billing solutions. Standalone billing services charge 3-8% of collections. ModMed gGastro and similar specialty solutions range from $500-750/provider/month.
What CPT codes are most important for GI billing?
Key GI CPT codes include colonoscopy (45378-45398), EGD (43235-43259), capsule endoscopy (91110-91111), and E/M codes (99202-99215). Proper modifier usage (-59, -XE, -22) is critical for colonoscopy with polypectomy reimbursement.
Does gastroenterology billing software integrate with endoscopy reporting?
Yes, specialty GI software like ModMed gGastro, gMed (now Modernizing Medicine), and Provation integrate directly with endoscopy reporting systems. This ensures procedure findings automatically populate billing codes and quality metrics.
What quality measures do GI practices need to report?
GI practices report MIPS quality measures including adenoma detection rate (ADR), cecal intubation rate, bowel prep adequacy, and appropriate surveillance intervals. Good GI software tracks these automatically from procedure documentation.
Should GI practices outsource billing or use in-house software?
Practices with 3+ providers often benefit from in-house billing software with trained staff. Smaller practices may prefer billing services charging 4-7% of collections. Hybrid approaches using software with RCM support are increasingly popular.
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