Provider Reimbursements and Audits

Hospitals participating in South Dakota Medicaid reimbursement programs submit Medicare Cost Report (MCR) information and related financial documentation to support reimbursement methodologies, rate development, cost settlement, and program administration.

Detailed information regarding hospital cost reporting requirements, submission guidance, and cost settlement processes is available on the Hospital Cost Reporting page.

Providers offering Behavioral Health, Substance Use Disorder, Child Protection, Prevention and other applicable DSS services can access cost report forms, instructions, training materials, and guidance in this section.

Department of Social Services Cost Reporting

PRA works with Department of Social Services programs to collect, review, and analyze provider cost reports used in reimbursement and rate-setting activities.

Resources

• Residential, Behavioral Health, and Prevention Providers Cost Report | Instructions
• Out-of-State PRTF Providers Cost Report
• Prevention-Only Cost Report | Instructions
• Training Materials
• Cost Report Updates and Guidance

For DSS Questions or Submissions
Email: DSSFinancePRA@state.sd.us

Department of Human Services Cost Reporting

Cost reports for nursing homes, assisted living facilities, nutrition providers, and homemaker providers are administered by the Department of Human Services (DHS).

Resources

Department of Human Services Cost Reports

For DHS Questions or Submissions

Email: DHSFinance@state.sd.us

This section applies to Federally Qualified Health Centers enrolled with South Dakota Medicaid.

Payment Methodologies

Federally Qualified Health Centers are reimbursed under one of two payment methodologies:

• Prospective Payment System: Federally Qualified Health Center services are reimbursed at the established encounter rate for covered services associated with a qualifying visit.
• Alternative Payment Method: Effective July 1, 2026, Federally Qualified Health Centers may elect to receive reimbursement under the Alternative Payment Method. The Alternative Payment Method provides enhanced encounter rates informed by statewide cost-based weighted average encounter rates. Providers must submit an Alternative Payment Method Election Form to participate.

For additional information, visit the Alternative Payment Method page.

Rate Updates

Provider Reimbursement & Audits annually:

• Reviews the Medicare Economic Index published by the Centers for Medicare & Medicaid Services.
• Updates applicable reimbursement rates in accordance with federal requirements.
• Coordinates implementation of approved rate updates.

This section provides South Dakota counties with reimbursement information and resources for the Catastrophic County Poor Relief Program.

Cost-to-Charge Ratio (CCR) Information

Provider Reimbursement & Audits calculates hospital Cost-to-Charge Ratios using information from hospitals' Medicare Cost Reports when available.

CCRs are updated annually and published for county reimbursement purposes under the Catastrophic County Poor Relief Program. Updated reimbursement information becomes effective July 1 each year.

PRA obtains Medicare Cost Report information from publicly available sources whenever possible. Hospitals may be contacted if additional information is needed to support CCR calculations.

When a CCR Is Not Available

If a hospital Cost-to-Charge Ratio is not available, counties may continue reimbursing eligible claims using the Medicaid reimbursement rate available through DSS.

CCR information is published annually and can be used when available for reimbursement calculations under the Catastrophic County Poor Relief Program.

County CCR Access Portal

South Dakota counties may log in to access hospital cost share information. You will need to enter your Username and Password.

• Call 605.773.3165 or email MedicaidClaimPricing@state.sd.us for more information or to receive a Username and Password.

County Claims Manual
Note: SDCL 28-13-28
Note: SDCL 28-13-31

Provider Reimbursement & Audits conducts financial review and monitoring activities to support program integrity, accurate reimbursement, and compliance with applicable state and federal requirements.

Subrecipient Monitoring

PRA conducts subrecipient monitoring activities for applicable pass-through grant programs in accordance with 2 CFR 200 and other applicable state and federal requirements.

Monitoring activities may include:

• Financial review procedures
• Compliance verification
• Supporting documentation review
• Corrective action follow-up, when applicable
  

Behavioral Health Billing Review

PRA conducts billing reviews of Behavioral Health providers to evaluate billing practices, verify supporting documentation, and promote compliance with program requirements.

Review activities may include:

• Documentation review
• Billing and financial analysis
• Sample testing procedures
• Review of reported services and expenditures

The items reviewed under a tentative schedule pursuant to SDCL 28-22 do not reflect statutory requirements for review. Items not mandated by statute are included to enhance transparency related to provider reimbursement methodologies.

Related information is available through the following resources:

• Rate Workgroups – Learn more about rate development workgroups and associated processes

Rate Review Cycles Page

The following items are reviewed on a tentative schedule pursuant to SDCL 28-22. Inclusion on this list does not indicate a statutory requirement for review. Items not mandated by statute are included to enhance transparency related to provider reimbursement methodologies. For more information on the rate review cycles please visit the Rate Workgroups page.

Service	FY23	FY24	FY25	FY26	FY27	FY28	FY29
Inpatient Hospital Services
Outpatient Hospital Services
Ambulatory Surgical Centers
Federally Qualified Health Centers and Rural Health Centers
Psychiatric and Intensive Residential Services
Substance Use Disorder Services
Mental Health Services Community and Independent
Behavioral Health Prevention Services
Criminal Justice/Juvenile Justice Initiative
Dental Services

This section is for hospitals required to complete the annual Disproportionate Share Hospital survey.

The annual Disproportionate Share Hospitals survey is used to collect information necessary to determine hospital eligibility for DSH payments.

Participating hospitals are required to complete and submit the survey each year, including providers that may not expect to qualify for payment.

DSH Survey Submission

DSH 2026 Survey

Includes:

• Survey workbook
• Instructions and submission guidance
• Reporting requirements
• Submission deadlines

Completed surveys should be submitted electronically to:

• DSSFinancePRA@state.sd.us

Subject line format:

• “DSH 20XX Survey – [Hospital Name]”

Reporting Guidance

Survey information should be completed using the provider’s most recent available cost report data and applicable reporting instructions.

Survey requirements and data sources may be updated periodically to align with federal DSH audit and reporting requirements.

Provider Reimbursement & Audits
700 Governors Drive
Pierre, SD 57501

DSSFinancePRA@state.sd.us
605.773.3643