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Physician bookkeeping: MPC books that reconcile to every OHIP remittance

An incorporated physician's books should start from gross billings and the OHIP remittance advice, not from the monthly deposit. Recorded that way, rejected claims, billing-agent fees, and overhead shares all stay visible — and your MPC has the clean corporate records that salary-versus-dividend planning depends on. That is how we keep books for physicians.

By the AnalytIQ Accounting team · Last reviewed: August 12, 2026

Physician consulting with a patient in a clinic exam room

Your MPC's books are more than one deposit a month

OHIP pays once a month, and it is tempting to treat that deposit as the whole story. It is actually the last step of a pipeline: services rendered, claims coded and submitted, some paid in full, some cut back, some rejected outright. Books that begin at the deposit can never tell you how much of your work went unpaid — and for a busy practice, that number is rarely zero.

We record gross billings as revenue with a claims receivable, then clear that receivable against the monthly remittance advice. The result is a ledger where billed, paid, and outstanding are three distinct figures your medicine professional corporation can actually act on.

Remittance reconciliation: billed, paid, rejected, stale-dated

Each month we match the RA against submitted claims, whether you bill through your EMR over MC EDT or through a billing agent. Underpayments and error codes get flagged back to whoever does your billing while the claims can still be corrected — Ontario gives you six months from the date of service to submit, and a rejected claim that sits past that window becomes a permanent write-off.

  • Rejection tracking — a running view of rejected dollars, so a coding problem shows up in month two instead of at year-end.
  • Agent statements — if a billing agent takes a percentage, we book revenue gross and their fee as an expense. Netting it away hides your true cost of getting paid.
  • Write-off discipline — stale or abandoned claims are written off deliberately, dated and documented, never silently absorbed.
  • Locum tracking — physicians working across several clinics or hospitals get a stream per site, so each location's billings, overhead, and travel stand on their own.

Not all practice income is OHIP — or HST-free

Most physicians have three or four income streams beyond fee-for-service, each with its own bookkeeping and GST/HST character. Mixing them into one revenue line makes both the tax treatment and the planning picture blurry.

Income streamHow it arrivesHow we book it
OHIP fee-for-serviceMonthly RA and depositExempt supply; gross billings with a claims receivable
Uninsured services and block feesPatient payments for forms, notes, annual plansOwn revenue line; taxability depends on purpose, so we tag each type
Medico-legal work and third-party examsInvoices to law firms and insurersGenerally taxable; tracked against the $30,000 small-supplier threshold
Hospital stipends, on-call, AFP paymentsContract payments on their own schedulesSeparate stream, reconciled to the underlying agreement
US locum or telehealth incomeUSD deposits from US entitiesConverted to CAD at proper rates and kept separate for treaty reporting

Overhead-share arrangements need their own ledger discipline

Group practice overhead is where physician books most often go muddy. Whether you pay the clinic a percentage of billings or a fixed cost share, we record your revenue gross and the overhead charge as its own expense, then reconcile it monthly against the clinic's statement — so a percentage that quietly drifts upward gets noticed.

If you are on the other side of the arrangement and collect overhead from other physicians, those charges are usually taxable supplies even though your clinical income is exempt. That combination catches many principals off guard, and it is exactly the kind of thing month-to-month books should surface rather than a CRA letter.

Month-end that feeds real planning

CMPA dues, college fees, CME travel, and private health premiums each have their own deductibility story, so we keep them in distinct accounts rather than one professional-fees bucket. If the MPC holds an investment portfolio, we record the activity monthly and reconcile the broker statements, because passive income inside the corporation can grind down access to the small business deduction — a number your accountant needs current, not reconstructed.

Salary versus dividends, the corporate investment account, passive-income limits on the small business deduction — every one of those decisions is made from the MPC's books, and a backlog of unreconciled months means planning from stale data. We close monthly, keep shareholder transactions out of the operating accounts, and hand your tax planner numbers that are current. See our tax services for the planning layer, and if your history includes US residency years, fellowship income, or American retirement accounts, our cross-border tax guide for physicians covers the reporting your books need to support.

Common questions.

Should my books show the OHIP deposit or my gross billings?

Gross billings, with a receivable cleared against each remittance advice. Booking only deposits hides rejected and underpaid claims, which are recoverable if caught within the six-month submission window.

My billing agent takes a percentage — how does that appear in the books?

Revenue is recorded gross and the agent's fee is a separate expense. Netting the fee out of revenue understates both your practice size and your true collection cost.

Is any of my income subject to GST/HST as a physician?

Clinical services are exempt, but medico-legal reports and most third-party exams are generally taxable. We track that stream separately so you know where you stand against the $30,000 registration threshold.

Related reading

A ledger that matches every remittance.

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