Dental tax

    CPA for dentists and 1099 dental hygienists

    Dental practice owners juggle payroll, entity choices and owner salary. Hygienists who temp through apps or work for several offices get 1099s with no tax withheld. Here is how the taxes work for each, and where planning helps.

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    • Last reviewed October 10, 2026
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    How do taxes work for a 1099 dental hygienist?

    A 1099 dental hygienist is self-employed, so no tax is withheld and you pay income tax plus 15.3% self-employment tax through quarterly estimates. You can deduct business costs like license fees, CE and malpractice insurance. Your Virtual CPA, a licensed CPA firm, prepares returns and plans taxes for hygienists and dental practice owners. Request a free consultation to get started.

    1099 or W-2: which are you?

    Whether a hygienist is an employee or an independent contractor depends on the facts. The IRS weighs three categories:

    • Behavioral control. Does the office control what you do and how you do it?
    • Financial control. Who sets your pay, covers expenses and supplies the equipment?
    • Type of relationship. Is there a contract, benefits, or an ongoing expectation of work?

    If you are unsure, you or the office can file Form SS-8 to ask the IRS for a determination. Practice owners who hire hygienists should apply the same test before issuing a 1099.

    For 1099 hygienists: estimates and deductions

    Quarterly estimates. With no withholding, you pay income tax and self-employment tax through Form 1040-ES. Self-employment tax is 15.3%: 12.4% for Social Security and 2.9% for Medicare. See quarterly tax planning.

    Deductions. Business expenses must be ordinary and necessary. Common ones for independent hygienists:

    • License and registration fees.
    • Continuing education that maintains or improves your skills.
    • Liability and malpractice insurance.
    • Scrubs, loupes and supplies used only for work.
    • Travel from one office to another on the same day. Commuting from home to a regular office is not deductible.

    W-2 hygienists generally cannot deduct unreimbursed job expenses on their federal return. If you work both W-2 and 1099 shifts, only the 1099 side carries business deductions.

    Many hygienists file extensions while they sort out 1099s from several offices. See extension filers.

    For practice owners: S corporations, salary and retirement plans

    S corporation and reasonable compensation. An S corporation owner who works in the practice must take reasonable W-2 compensation before taking distributions. IRS factors include training and experience, duties, time devoted to the practice and what comparable practices pay. See S corp reasonable compensation and LLC vs S corp.

    Retirement plans. A SEP is funded only by the employer, and the practice must contribute the same percentage for every eligible employee. A one-participant 401(k) is for an owner with no employees other than a spouse, so it fits an independent hygienist or solo practitioner, not a practice with staff.

    Books and payroll. Clean monthly books make quarterly estimates and year-end planning straightforward. See medical and dental practice accounting.

    How it works with us

    Best for: dental practice owners and associates, and hygienists paid on 1099, W-2 or both, including those who work through staffing apps.

    1. Free initial consultation. Tell us how you are paid and what you need help with.
    2. Fees quoted upfront, in writing. Transparent, fair fees before any work starts.
    3. Review. We review last year’s return, your 1099s and W-2s, and your books if you own a practice.
    4. Plan. Quarterly estimates, deductions to track, and entity and salary recommendations for owners.
    5. File. We prepare and file the returns and set up next year’s estimates.

    Hygienist on 1099 vs W-2 vs practice owner

    SituationReturnsEstimated taxesKey planning items
    Hygienist on 1099Form 1040 with Schedule C and Schedule SEUsually yes, quarterly on Form 1040-ESTrack deductions, set aside self-employment tax, consider a SEP or one-participant 401(k)
    Hygienist on W-2Form 1040Usually no; tax is withheldCheck withholding (Form W-4); ask for reimbursement of work costs
    Practice owner (S corporation)Form 1120-S plus owner’s Form 1040 with Schedule K-1Often, for income above withholdingReasonable salary, payroll, retirement plan for staff, state taxes

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    Dental practice owner or 1099 hygienist? Tell us how you're paid and we'll set up a free initial consultation.

    Frequently asked questions

    Usually, yes. No one withholds tax from 1099 pay, so you pay income tax and self-employment tax yourself through quarterly estimated payments on Form 1040-ES. Self-employment tax applies once your net earnings reach $400 for the year.

    It depends on the facts, not the label. The IRS looks at behavioral control, financial control and the type of relationship. If the office sets your schedule, supplies the equipment and directs how you work, that points toward employee status. Either party can ask the IRS to decide by filing Form SS-8.

    Ordinary and necessary business costs, such as license and registration fees, continuing education that maintains or improves your skills, liability or malpractice insurance, scrubs and loupes used for work, and travel between two offices on the same day. Commuting from home to a regular office is not deductible.

    Generally, no. Unreimbursed employee expenses are no longer deductible on the federal return for most employees. Ask your employer to reimburse work costs under an accountable plan instead.

    Often it is worth reviewing once profit is well above what you would pay yourself as salary. As an S corporation owner you must take reasonable W-2 compensation before distributions. We run the numbers for your practice, including payroll costs and state rules, before you elect.

    An extension gives you more time to file, not more time to pay. Any tax still owed after the April deadline accrues interest. We can finish the return and set up next year’s estimates so the balance does not repeat.