If you're switching to Cliniko from Halaxy, then here are the details you’ll need in order to transfer your data into your Cliniko account!
☝️ Please note that this data transfer service is a process that we will work on with you—not something that you'll need to do yourself. Please don't import spreadsheets or manually add any information into your Cliniko account before the transfer, as duplication will result when your data comes across from Halaxy.
The very first step is booking your transfer date! We sometimes book months in advance, so we strongly recommend you book as soon as you can to avoid further delays:
Once you've done that, please read through the guide below. It's important to review each section thoroughly, as it outlines your role in the transfer, and what we do for you.
The guide is broken into the following sections:
Getting familiar with Cliniko
For a smooth transition, please ensure that your team has had an opportunity to play around with Cliniko and are familiar with it. The trial is unrestricted, so all features are available to set up and become familiar with. You can change your subscription level as required while trialing, which will let you add more practitioners!
In case it's useful, these training guides might come in handy:
All of our support articles and guides can be found on our help site, too! You can quickly search for anything you’d like help with right here.
All users are encouraged to contact our support team with any questions. We're easiest reached from within Cliniko by clicking Help on the blue sidebar, and clicking Chat with us! If you'd prefer email, you can reach us at firstname.lastname@example.org.
Exporting data from Halaxy
To obtain the data to import into Cliniko, you’ll need to export a backup directly from your Halaxy account using their export feature. You'll need to have full data exporting enabled by Halaxy first. You can find instructions on exporting from Halaxy on their help site. Please ensure that you select all checkboxes under Export My Data. Once your backup has completed, you can download the zip file.
☝️ Note that any data entered into Halaxy after this export will not be transferred to Cliniko, as it won't be included in the exported data. This data will need to be noted and manually entered into Cliniko after the transfer has been completed.
If a practitioner only wants to export their own data, you can change the access levels of that practitioner from Clinical access to Personal access. That practitioner will then be able to export only the data relating to them. This can be done within Halaxy from Settings → Users and updating the access levels by clicking on the Edit (pencil) icon against the name of the practitioner. More info from Halaxy here.
Your Halaxy export may be very large, depending on your volume of patients, files, treatment notes, and so on. We won't be able to transfer any data into your Cliniko account until you've shared the Halaxy export with us.
Once you have your exported data, please upload the entire zip file to your preferred cloud storage service (Microsoft OneDrive, Google Drive, Dropbox, etc), and share with us from there. Contact us for more info.
At a minimum, please perform your export, download it, and upload it to your chosen storage option by the day before your scheduled transfer, so that we have time to download your exported data. It's important to have all these steps completed prior to the transfer, as we still require time on the day of transfer to load and prepare your data in our system to then be written into your Cliniko account.
Setting up your Cliniko account
There's a bit of setup required in Cliniko prior to the transfer. These are things that we can't necessarily determine or transfer from Halaxy, or settings that are specific to Cliniko.
Please ensure the following things are set up as soon as possible:
All sites/locations of your business are set up as Cliniko business locations,
Your time zones have been set correctly (to ensure that appointments get transferred to the right spots), and
Mobile phone numbers have been added to the admin user's account so that we can authenticate prior to transfer.
Other items that are not required prior to transfer, but are not transferred and will need to be set up manually are:
All treatment note templates are created,
All letter templates are created,
All appointment types are created and set up (assign practitioners, assign colours, relate billable items and treatment note templates, assign reminder and confirmation templates).
Note that when we transfer appointments, we will need a practitioner assigned to the appointment. This is a little complicated for instances where the practitioner is no longer with you and therefore not in Cliniko. In these cases, please let us know whether you would prefer to assign the appointments to:
A generic ‘Former practitioner’ that you create in Cliniko,
Another active practitioner in Cliniko, or
Exclude them entirely.
Alternatively, you may create all your specific members of staff (past and present) in Cliniko, and we’ll assign all appointments correctly. You can set those former practitioners as inactive, as your Cliniko subscription price is based on the total number of active practitioners.
Finally, Cliniko limits the volume of patient attachments in trial accounts. To remove this limit, please add your billing details into your account. Your free trial will continue until completion, and your credit card will not be charged until your trial period has expired.
You can quickly search for and find our guides and help articles to assist you with the setup process on our help site, here.
If you'd like any assistance with getting set up, feel free to contact us! Even if you just have a quick question that you’d like an answer for, we are easiest reached from within Cliniko by clicking Help on the blue sidebar, and clicking Chat with us! You can also click the chat "bubble" at the bottom right corner of this page.
What do we transfer?
Note that no data is removed from Halaxy in the transfer process. Data is copied to your Cliniko account. The types of data that are transferred are not customisable.
Transfer to Cliniko will include the following from your Halaxy export:
Clinical records (transferred as PDF files under Cliniko patients)
Contacts (referrers, specialists, organisations)
Transfers can take anywhere from a few hours to a day, depending on the volume of data being transferred.
Prior to the data transfer, please avoid creating any Patients or Contacts.
We will import all of these as part of the Halaxy transfer. If that data is already in Cliniko, it will be duplicated.
What don’t we transfer?
Unfortunately, all financial details are excluded from transfer. There is not a way to import financial data into Cliniko. This includes:
Appointment invoice/payment statuses
The only exception to this is that the invoice line items for each appointment will appear in the appointment note for each historical appointment that is transferred.
If you'd like to record prior payment history or outstanding debts in Cliniko, you can create an opening balance for those patients. This is not considered revenue and will not affect Cliniko's reporting.
In addition, the following items are not transferrable and must be set up manually where needed:
Users and practitioners, practitioner reference numbers
Businesses locations and settings
Expenses and stock sales
3rd party app integrations
Letters and letter templates
Patient forms and form templates
Communication templates (email and SMS)
Information that we'll need from you
When you book a transfer date, you'll be sent a confirmation email which includes a link to a secure electronic form. This form is where the below information is collected from you. If you miss the confirmation email, another link to the same form will be sent in a reminder email closer to your transfer date. Please let us know if you do not receive these emails.
The following are some questions we need to know to accurately transfer data into Cliniko. If you are unsure of the answer, please seek clarification.
Do you have any practitioners in Halaxy who are inactive?
If so, we will need to determine what to do with appointments assigned to them. There are a couple of options here:
We can leave those appointments behind and not transfer them into Cliniko.
You can create all your inactive practitioners in Cliniko, and we can assign appointments to the correct practitioner. You can make these practitioners inactive in Cliniko prior to transfer, so they do not contribute to your subscription plan.
You can elect one or more other practitioners in Cliniko to assign those appointments to (e.g. use an existing practitioner, or create one practitioner named “Old Halaxy practitioner”, or similar). You'll just need to tell us which practitioner/s in Halaxy you want mapped to which practitioner/s in Cliniko.
Which appointment type would you like to use for your historical Halaxy appointments?
Appointment types are unable to be transferred from Halaxy, so please let us know the desired appointment type name that you wish your Halaxy appointments to be created as in Cliniko. It could be anything you'd like, from "Appointment", to "Transferred Halaxy Appointment", keeping in mind that if you have appointment type placeholders in any of your confirmation or reminder templates, that the appointment type name will be shown there.
Accessing your Cliniko account
In order to access your new Cliniko account and write your data to it, we’ll need your Cliniko URL and an API key. When you book a transfer date, you'll be sent a confirmation email which includes a link to a secure electronic form. This form is where this information is collected from you. If you miss the confirmation email, another link to the same form will be sent in a reminder email closer to your transfer date. Please let us know if you do not receive these emails.
Your URL can be found in your browser address bar when you're logged in to Cliniko, and will look something like
https://your-clinic.au2.cliniko.com. This is required so that we may be sure we’re transferring data to the correct account.
Cliniko API key
Please log in to your Cliniko account to generate the API key. You'll need to be logged in as an administrative user who is also a practitioner so that the API key generated has the required data access permissions. Please also see our guide on generating a Cliniko API key.
☝️ To have the correct permissions, the API key must belong to a user who is also a practitioner. Please do not give us an API key for an administrator that is not also a practitioner.
Your API keys are like passwords, and must be handled with care. It's very important that this information is transmitted to us securely. When you book a transfer date, you'll be sent a confirmation email which includes a link to a secure electronic form. This form is where you can safely communicate your API keys and other information to us. If you miss the confirmation email, another link to the same form will be sent in a reminder email closer to your transfer date. Please let us know if you do not receive these emails.
Administrator mobile numbers
We’ll also need to do some verification of an account administrator to get the final go-ahead to access the account and load data, so please ensure a mobile numbers are included in user's profiles so we can send a verification code to the required user.
On the day of the transfer
As a reminder, uploading your Halaxy backup will take time, and transfer into Cliniko cannot start until that backup is uploaded to us. If this process is only able to start on the morning of transfer, your actual transfer may not commence until much later in the day. Accordingly, please schedule export and upload at least one day prior to your transfer.
We shouldn’t need to hassle you much on the day of the transfer, unless some of the above information or setup is missing, so please ensure you are contactable on the day. We’ll get started in the morning (AEDT) and let you know when we are done! If it looks like things will take longer than the day, we’ll be sure to reach out and keep you informed of the progress.
When the transfer is completed, you’ll be able to use your data within Cliniko immediately.
If there’s anything you’d like to confirm or discuss prior to transfer, please do let us know—we’re here to help!
The final checklist
Having all of this done before the transfer takes place is super important. Please be sure that each item on these lists has been checked off prior to your transfer date!
Please be sure that you have completed the following:
The transfer date has been booked
The export of data from Halaxy has been arranged
The exported Halaxy data has been uploaded to your chosen online storage, and a share link given to the Cliniko team
On the Cliniko side of things:
[Required] Practitioners have been created, both active and inactive (see guide)
[Strongly recommended] All administrator user accounts have mobile numbers
[Required] Business locations have been created, both active and inactive (see guide)
[Required] You have added a payment method to your Cliniko subscription, to lift the file upload limitation (see guide)
After transfer, these items will need attending to:
Ensure all required appointments types are created (see guide)
Set practitioners as providers of appointment types (see guide)
Create treatment note templates (see guide)
Create letter templates (see guide)
Create billable items (see guide)
Relate billable items to appointment types (see guide)
Relate treatment note templates to appointment types (see guide)
We know that transferring from another system is a big deal, and we want to help make the process as easy as possible for you. If you have any questions on anything at all, please reach out to us. We're always available to help!