The tax office can inspect you years after you filed the return. If you cannot produce the documents it asks for, you have a problem: the tax administrator is entitled to estimate your tax, and the estimate almost never goes in your favour. Here is what you have to keep, for how long, and how to stay ready for an inspection you did not see coming.
Why this matters more than it looks
Keeping documents is not just paperwork for its own sake. It is your insurance against a financial loss. In a tax inspection the burden of proof sits with you: you have to show that your income and expenses match what you put in the return. Without documents you cannot.
The tax office can open an inspection at any point within the assessment period — normally three years from the end of the deadline for filing the return, but it can stretch to ten. If you do not produce the documents during the inspection, the tax administrator proceeds under Section 98 of the Tax Code and assesses the tax using aids, which is to say by estimate. That estimate is usually higher than what you actually owed.
Retention periods by document type
Tax documents (invoices) — 10 years
Under Section 35 of the VAT Act (Act No. 235/2004 Coll.), a registered VAT payer must keep tax documents for 10 years from the end of the tax period in which the supply took place. In practice:
- An invoice issued in March 2025 — keep until the end of 2035
- An invoice issued in December 2025 — keep until the end of 2035
- An invoice issued in January 2026 — keep until the end of 2036
The period covers all tax documents: invoices issued and received, simplified tax documents, corrective tax documents and documents for payments received in advance. Ten years is long, but there is a reason for it — in certain cases the tax office can reach back to older periods.
Records of income and expenses — at least 3 years
If you keep tax records rather than full accounts, which is the case for most self-employed people, Section 7b of the Income Tax Act requires you to keep them for as long as the period for assessing the tax has not expired. In practice that means at least 3 years from the expiry of the filing deadline, but the period can be extended — by the opening of an inspection, by a supplementary return and so on.
Recommendation: even though the law says three years, keep your tax records for five to seven. The period stretches for all sorts of reasons and you do not want the surprise. If you are a registered VAT payer, the ten-year period for tax documents catches you anyway.
Accounting records — 5 years
If you keep double-entry accounts — compulsory for companies, voluntary for the self-employed — the Accounting Act (Act No. 563/1991 Coll.) sets these periods in Section 31:
- Financial statements and the annual report: 10 years from the end of the accounting period they relate to
- Accounting documents (invoices, cash documents, bank statements): 5 years from the end of the accounting period
- Accounting books, depreciation plans, inventory lists: 5 years
- The chart of accounts and summaries: 5 years
Careful: for registered VAT payers the 10-year period from the VAT Act and the 5-year period from the Accounting Act overlap. The longer one always wins — 10 years for tax documents. Follow the longest applicable period; a shorter one in one statute does not release you from an obligation set by another.
Payroll sheets and payroll records — 45 years
If you have employees, payroll sheets and everything needed to calculate a pension must be kept for 45 years (extended from 30 years as of 1 January 2023). The obligation comes from Section 35a(4) of the Act on the organisation and administration of social security (Act No. 582/1991 Coll.). It is the longest retention period you will meet in practice. Payroll sheets are the basis for calculating your employees' pensions, and losing them has consequences beyond your own tax position.
Contracts
There is no single retention period for contracts. The general rule: keep a contract for the term of the relationship plus the limitation period. The general limitation period under the Civil Code is three years (subjective), but claims can run up to fifteen years (the objective limitation period for damages). In practice, keep contracts for at least ten years after the relationship ends, particularly contracts for work, leases and anything with a high value.
What to keep: a checklist for the self-employed
Invoices and tax documents issued
Keep copies or originals of every invoice you issued. For electronic invoices the digital form (PDF) is enough. Every invoice has to carry all the particulars required by law — Section 29 of the VAT Act for registered payers. Keep invoices for exempt supplies and for supplies with a place of supply outside Czechia too.
Invoices and receipts received
Keep the originals of every invoice and receipt that supports an expense. Thermal-paper receipts, typically from tills, are a special case — the print fades completely with time, often within six to twelve months. Scan or photograph them straight away; the scan then serves as evidence once the original has gone blank.
Bank statements
Every statement from business and personal accounts, if you claimed expenses paid from the personal one. Most banks keep an archive in internet banking, but check how far back it goes — it may not be ten years. Some banks keep only five to seven. Download your statements regularly and keep them in an archive of your own.
Contracts and orders
Signed contracts with clients, suppliers and landlords. Orders and order confirmations. Framework agreements, amendments and annexes. Anything that shows a business relationship existed and on what terms — especially where those terms differ from ordinary commercial practice, such as unusual prices or non-standard payment conditions.
Returns and statements
Copies of every tax return you filed, VAT returns included, and of the přehled — the annual statement for the social security office and your health insurer. If you file through a data box, keep the delivery receipt. For filings through EPO, keep the acknowledgement of receipt. These are what prove you filed on time.
Correspondence with the tax office
Everything: requests, decisions, payment assessments, inspection protocols, your replies. Keep both what you received and what you sent. For data messages, download and store the content and the attachments — messages in a data box are deleted automatically after 90 days unless you pay for the Datový trezor (data vault) service.
VAT records
If you are a registered VAT payer, keep in addition:
- The VAT records required by Section 100 of the VAT Act
- The VAT control reports and VAT returns you filed
- EC sales lists, if you supply to the EU
- The documents that support your right to deduct VAT
Digital archiving
Physical files still count, but more and more entrepreneurs have moved to digital archiving, and the law fully allows it.
The legal framework
Keeping documents in electronic form is fine as long as you can show the authenticity of their origin, the integrity of their content and their legibility for the whole retention period — the conditions Section 35(3) and the following provisions of the VAT Act set for tax documents. Authorised conversion, which gives a scan the legal force of the original, is governed by Section 22 of Act No. 300/2008 Coll.; for the ordinary documents of a self-employed person you do not need it. The conditions for valid digital archiving:
- Integrity — the document must not change after digitisation. Ideally add a qualified electronic signature or a qualified time stamp. For the ordinary practice of a self-employed person, plain digitisation (a scan or a photo) kept in an unchangeable form is enough.
- Legibility — the scan has to be good enough to read. At least 300 DPI, in PDF or PDF/A.
- Long-term availability — the documents have to stay accessible for the whole retention period. That means working storage and regular checks that the data is still intact.
How to do it well
- Use PDF/A — the PDF/A format (ISO 19005) is designed for long-term storage. An ordinary PDF can contain elements, such as fonts and scripts, that may not be supported in the future. PDF/A forbids them and guarantees the document stays readable.
- Keep an organised folder structure — split by year and type: 2025/invoices-issued, 2025/invoices-received, 2025/bank-statements. Name files systematically: date, document number, counterparty. A consistent system saves hours during an inspection.
- Back up in more than one place — at least two independent ones. Cloud storage plus a local backup on an external drive, or two different cloud services. The 3-2-1 rule: three copies of the data, on two types of media, one of them off site.
- Cloud storage is legally fine as long as the integrity requirements are met. It gives you access from any device, automatic backup and protection against fire, flood and theft.
What to do with electronic invoices
Invoices issued and received electronically — as a PDF by e-mail, or through an invoicing system — do not have to be printed. Keep them in their original digital form. In fact printing an electronic invoice and deleting the original can create a problem, because the printout does not have the same evidential value as the electronic original with its digital signature or demonstrable origin.
For electronic invoices, check that:
- The invoice is stored in an unchangeable form, not only in an e-mail you might delete
- It will stay legible for the whole retention period
- You can show where it came from — the e-mail exchange, a record in the supplier's system
What happens when you cannot produce the documents
Failing to produce documents in a tax inspection leads to one of the least pleasant scenarios in Czech tax procedure. Here is what is at stake.
Assessment using aids (Section 98 of the Tax Code)
The tax office can assess your tax using aids, which means by estimate. The aids can be:
- Figures from your earlier tax periods
- Figures from other taxpayers doing comparable work in the same area
- The tax administrator's own findings, for example from a local inquiry
- Data from publicly available sources
In practice the tax office can take the average margin in your field and estimate your income from the turnover on your bank account. Expenses you cannot document simply will not be accepted. You can appeal against an assessment using aids, but the success rate is low: you would have to prove that the aids were wrong, which without documents is close to impossible.
Disallowed expenses — the usual outcome
If you cannot produce documents for your expenses, the tax office disallows them. Your tax base goes up, possibly by a lot, and the assessed tax goes up with it.
A worked example
A self-employed person with income of CZK 1,200,000 claimed real expenses of CZK 800,000. Tax base CZK 400,000, tax CZK 60,000. During an inspection they cannot produce documents for CZK 300,000 of those expenses, and the tax office disallows them. New tax base CZK 700,000, tax CZK 105,000. The shortfall is CZK 45,000, plus a penalty of 20 % (CZK 9,000), plus late payment interest running from the original due date. Around CZK 60,000 and up in total — because of missing paperwork.
Note: in this example the person could switch to flat-rate expenses if they qualify, since 60 % of income (CZK 720,000) is higher than the expenses they can actually document (CZK 500,000). That is a last resort, though — the tax administrator does not have to accept a change in the method of claiming expenses after the fact.
Retention periods at a glance
- Tax documents (invoices of a registered VAT payer): 10 years from the end of the tax period
- Tax records of a self-employed person: at least 3 years, 5 to 7 recommended
- Accounting documents (double-entry accounts): 5 years from the end of the accounting period
- Financial statements and the annual report: 10 years
- Payroll sheets and payroll records: 45 years
- Contracts: the term plus the limitation period, 10 years after the end recommended
- Correspondence with the tax office: 10 years, recommended
- Returns and annual statements filed: 10 years, recommended
- VAT control reports and VAT returns: 10 years
Practical tips
- Digitise on the day — scan or photograph each document when you receive it. Thermal receipts fade in months. Make a habit of it: document in hand, phone out, photo, saved.
- Use one naming convention — date, document number, supplier or customer. For example: 2025-03-15_FV2025-042_SupplierName.pdf. With a consistent name you find anything in seconds.
- Automate what you can — invoicing software stores and organises the invoices you issue. Get incoming invoices into the system straight away rather than leaving them in your inbox.
- Check the backups — at least once a year, confirm that they are complete and readable. Open a few files at random and make sure they are not corrupted.
- Do not throw anything away early — when in doubt, keep it. Storage costs almost nothing compared with a missing document during an inspection. A single undocumented expense of CZK 50,000 can cost you more than CZK 15,000 in extra tax, insurance and penalties.
- Separate business from personal — keep two systems. It prevents the mess and speeds up any preparation for an inspection.
Getting ready for an inspection
If your archive is in order, a tax inspection is not something to fear. A few practical points:
- Keep documents in chronological order — the inspector will appreciate it, and it speeds the whole thing up.
- Prepare a summary of the key items — the biggest invoices, unusual transactions, investments. These are what inspectors look at first.
- Check consistency — do the invoice totals match the bank statements? Do the records match the return you filed?
- Do not panic — an inspection is a routine act, not a punishment. Cooperate, be helpful, and hand the documents over on time.
Taxorio keeps your invoices, expenses and the files you attach to them in one place, filtered and searchable, with the mobile scan for receipts before they fade. When an inspection comes, you pull the documents out of the app rather than out of a box. Try it at app.taxorio.cz — and keep your own backup of the exports as well, because a retention period outlives any single tool.
Taxorio scope: Taxorio provides invoicing and income/expense records for Czech sole traders. It is not full accounting or personalised tax advice. For an unsupported or unusual case, verify the treatment with a Czech accountant or tax adviser before filing.