Chart of accounts for a medical practice, with a worked month for a small clinic

A medical practice needs a normal small business chart of accounts plus a handful of practice-specific ones: patient revenue split into insurance and patient payments, a contra account for refunds, merchant fees, medical supplies, malpractice insurance, practice software, and owner pay kept apart from wages. About 35 to 45 accounts covers most small clinics. Below is a numbered starting chart and one made-up month booked against it.

A starting chart

Numbers in the 1000s are assets, 2000s liabilities, 3000s equity, 4000s revenue, 5000s and up costs and expenses. Leave gaps so you can add accounts later without renumbering.

Number	Account	Notes
1010	Operating checking	One account per bank account
1020	Payroll checking	If payroll runs from its own account
1500	Medical equipment	Tables, imaging, chairs, at cost
2010	Business credit card	One per card
2100	Payroll liabilities	Withholdings and employer taxes owed
2500	Equipment loan	Matched to the lender's statement
3100	Owner contributions	Money the owner put in
3200	Owner draws	Money the owner took out, if not paid through payroll
4010	Patient service revenue: insurance	Payer deposits
4020	Patient service revenue: patient payments	Copays, deductibles, self-pay, gross of card fees
4090	Patient refunds	Contra revenue: overpayments returned
5010	Medical supplies	Disposables, exam supplies
6010	Wages	Staff gross pay, from the payroll report
6020	Payroll taxes	Employer share
6100	Rent
6200	Merchant fees	Card processor fees
6300	Malpractice insurance
6400	Practice software	EHR, scheduling, clearinghouse
7010	Interest expense	The interest part of loan payments

Two accounts on that list do most of the work. 4020 is recorded gross, so card fees show up in 6200 instead of quietly shrinking revenue. 4090 keeps refunds out of expenses, where they would make the clinic look busier and more expensive than it is.

A worked month: Summit Spine Chiropractic

Summit Spine Chiropractic is fictional: a one-chiropractor clinic with two staff, set up as a single-member LLC, cash-basis books. The owner takes draws rather than a salary. Here is its August 2026 operating checking statement and where each line went:

Statement line	Amount	Booked to
Insurance EFTs, 4 payers	11,260.00	4010 Insurance
Card processor deposits	6,384.42	4020 Patient payments 6,580.00, 6200 Merchant fees 195.58
Cash patient payments deposited	420.00	4020 Patient payments
Refund, overpaid deductible	(120.00)	4090 Patient refunds
Rent	(3,200.00)	6100 Rent
Medical supply order	(486.30)	5010 Medical supplies
Payroll, net pay	(8,940.00)	6010 Wages, from the payroll report
Payroll taxes	(2,410.00)	2100 and 6020, from the payroll report
Transfer to owner	(4,000.00)	3200 Owner draws

The card deposits

The processor's monthly statement shows 6,580.00 of patient card payments and 195.58 of fees. The bank shows what was left: 6,580.00 − 195.58 = 6,384.42. Booking the deposit as revenue would hide 195.58 of cost and understate revenue by the same amount. Over a year that's well over two thousand dollars of fees nobody sees.

Revenue for the month

11,260.00 + 6,580.00 + 420.00 − 120.00 = 18,140.00 of net patient revenue. The bank received 11,260.00 + 6,384.42 + 420.00 − 120.00 = 17,944.42. The difference is the 195.58 the processor kept.

Payroll

The bank shows 8,940.00 of net pay and 2,410.00 of tax payments. Neither is the wage expense. The payroll report gives gross wages, what was withheld from staff, and the employer's own taxes. Withheld amounts are owed to the government on staff's behalf, so they move through 2100 Payroll liabilities; only gross wages and the employer share are expenses. Book from the report, not the bank.

The owner

The 4,000.00 transfer is a draw. It doesn't reduce profit. In an LLC taxed as a sole proprietorship, the owner is taxed on the profit whether or not it was taken out. If Summit Spine later elects S corporation status, the owner would go on payroll for a reasonable salary and this account would become distributions.

What the clinic sends each month

Bank and card statements as PDFs, the processor's monthly statement, the payroll report, and any loan or lease statements. If the owner wants revenue by insurer, a deposit total per payer from the billing system. No patient names and no charts. The books are built from financial documents only.

Doing it or handing it over

The full chart, a worked month for a two-owner physical therapy clinic and the questions owners ask about billing and patient data are on our bookkeeping for medical practices page.

Disclosure: I'm Damin and I run ZeraBooks. Our team keeps clinic books from exactly the documents above, uploaded to a portal; there's no bank feed and no connection to your billing or EHR system. Each month is proven against the statements before it closes, and you get a read-only login. Pricing starts at $150 a month (USD) and is set after a free call. See bookkeeping services.

Set up 4020 and 4090 first. They are the two accounts that make a clinic's profit and loss honest.