Payment reconciliation for clinical research

Every trial payment, reconciled to the line item.

The revenue cycle in clinical research is fragmented and manual. Invoice formats vary across sponsors, CROs, and sites, and payments are tied to milestones that shift over the course of a trial. Katalyst Payments reconciles them automatically — in whatever format they arrive.

Book a walkthrough → See how it works

Sponsors · CROs · Sites — one reconciliation layer, with a person on every exception.

The problem

Trial revenue is owed, agreed, and still unreconciled

Nobody disputes the work was done. The money just can't be traced to it — because every payer describes the same trial differently, and the schedule it was priced against has already moved.

Every payer has its own format

Sponsors, CROs, and sites each invoice and remit differently — PDFs, spreadsheets, portal exports. Nothing lines up column to column.

Milestones move

Payments are tied to milestones that shift over the course of a trial. The schedule agreed at start-up rarely survives to close-out.

Reconciliation is manual

Matching a remittance back to the line items it paid means reading documents side by side and keying the difference into a spreadsheet.

It costs your best people

The only staff who can interpret a trial budget are the same staff you need running the trial. Reconciliation quietly consumes them.

How it works

From whatever they sent you to a reconciled ledger

1

Ingest

Invoices, remittances, contracts, and budgets — in whatever format they arrive, from whoever sent them.

2

Normalize

Line items are read and mapped to one common schema, per study and per payer.

3

Match

Each line item is reconciled against the current milestone schedule — not the one agreed at start-up.

4

Flag

Variances, duplicates, and unbilled work are surfaced as exceptions with the source document attached.

5

Close

A reconciled ledger per study, with an audit trail behind every payment.

The reconciliation layer

Built for documents nobody agreed to standardize

Katalyst reads what your payers already send. No templates for your team to maintain, and no request for a sponsor to change how they invoice.

Any format in, one ledger out

The model reads the documents you actually receive — sponsor invoice PDFs, CRO remittance files, portal exports — and normalizes them into line items you can compare against each other.

  • ✓ Reads PDFs, spreadsheets, and portal exports as they arrive
  • ✓ Line items normalized per study and per payer
  • ✓ No format templates for your team to maintain
Ingestion
Sponsor invoice · PDF18 line items extracted
CRO remittance · CSVMapped across 3 milestones

Reconciled against milestones that actually moved

Milestone schedules drift, and a payment that looks short is often correct against a schedule that changed. Katalyst reconciles to the live schedule and shows what moved — so a shortfall is either explained or flagged, never quietly written off.

  • ✓ Reconciles to the live milestone schedule, not the start-up version
  • ✓ Variances explained line by line, with the source document attached
  • ✓ Duplicates and unbilled work surfaced before close-out
Exceptions
Matched to milestoneVisit 3 complete · paid in full
Flagged for reviewScreen-fail fee invoiced, not remitted

A person decides every close call

The model doesn't guess. Anything it can't reconcile with confidence becomes an exception with the evidence attached, so your team spends its time on the handful of judgement calls instead of the thousands of matches.

  • ✓ Confident matches close automatically
  • ✓ Everything else is queued as an exception, with its source
  • ✓ Full audit trail on every decision, automated or human
Review queue
Closed automaticallyMatched line items, no review needed
Sent to a humanJudgement calls, with evidence attached
For sponsors

You never touch the tool. You feel it anyway.

Sponsors don't interact with the reconciliation layer directly. What they get is a partner that doesn't have to dedicate skilled staff to wrangling spreadsheets — and a site whose payment questions arrive already answered.

No portal to learn No format change Fewer payment queries
  • ✓ Fewer payment queries coming back to your team from the site
  • ✓ Invoices that arrive consistent, in the format you already accept
  • ✓ Site staff spending their hours on the trial, not on reconciliation
  • ✓ Faster close-out, because the backlog never built up
9 monthsOf manual reconciliation work automated in the pilot

In its pilot phase, the reconciliation model worked through a backlog that would otherwise have taken a skilled team roughly nine months to clear by hand — invoice by invoice, line item by line item.

Gen AI reconciliation, with every exception routed to a person.

FAQ

Questions, answered

Who is this built for?

Research sites and site networks carrying the reconciliation burden themselves — and CROs managing site payments across a portfolio. If someone on your team reconciles trial payments in a spreadsheet, this replaces that work.

Do our sponsors or CROs have to change how they invoice?

No. That's the point. The model reads the formats they already send you — invoice PDFs, remittance files, portal exports — so nothing changes upstream.

What happens when the model isn't sure?

It doesn't guess. Anything it can't reconcile confidently becomes an exception with the source document attached, and a person decides. Confident matches close automatically.

How does it handle milestones that shift mid-trial?

It reconciles against the current milestone schedule rather than the version agreed at start-up, and shows you what changed — so a payment that looks short is either explained by a schedule change or flagged as a genuine variance.

Do sponsors use this directly?

No. Sponsors don't interact with the tool. They benefit indirectly, from a partner that isn't diverting skilled staff into spreadsheet work and from a site that raises fewer payment queries.

How do we get started?

Tell us how many studies you're running and how payments reach you today. We'll walk you through reconciliation on your own invoice formats.

Stop reconciling trial payments by hand.

Tell us how many studies you're running and how payments reach you today, and we'll walk you through reconciliation on your own invoice formats.