Clinical Notes


Clinical notes form part of a patient's health record in Halaxy and can be accessed from their patient profile page. Clinical notes allow you to add additional information on a patient to provide better treatment. You can view a list of a patient's clinical notes in their profile.

To save time, you can also create Clinical Note Templates for you and your practice group.

A referral acceptance letter is shown as sample clinical note template

A new clinical note is automatically created for every appointment and linked to the associated invoice. You can also create clinical notes manually and link the note to an appointment or referrals as needed.

Prescriptions and orders, as well as clinical tools, are also added as clinical notes to a patient's profile.

You can set your Calendar Preferences to show clinical note status as an icon on the appointment. This makes it easy to see at a glance whether or not you have saved and published the clinical notes for that appointment.


Image: Clinical note status shown by the coloured pencil icon

Creating clinical notes

Clinical notes are automatically created for each appointment. To create a clinical note manually, navigate to the patient's profile and click the Clinical Notes tab, then click New Clinical Note in the top-right.

You can then begin entering data into note you have created.


When an administrator creates a clinical note, they will have to select a practitioner to link to the note as it is not automatically assigned.

Accessing and viewing a patient's clinical notes

A patient's clinical notes are visible on the Clinical Notes tab on their patient profile. You can access the Clinical Notes tab in two ways:

  1. From a patient's profile: go to the patient's profile from your Patients List, invoice or your calendar, then click the Clinical tab; or

  2. From your Calendar: When an appointment has been made with the patient on your calendar, click the appointment on the calendar, then click Notes. You will be taken to the notes created for the specific appointment.

Practitioners with the appropriate level of access can also click the Social History tab on a patient's profile to view and edit their demographic background and details.

Searching for clinical notes

The Clinical Notes screen is structured so that you can see each of the patient's clinical notes on the left-hand side, with the current note that you are viewing in the centre.

On the left-hand column, click the Expand (+) icon next to "Update Note Filters" to access filters that you can use to search for clinical notes:

Filter settings for clinical notes, set to reverse chronological order

You can sort by Chronological or Reverse Chronological order, set From and To date filters, and filter by the type of Clinical Note.

Click Save to activate your filters.

Formatting clinical notes

Once you have created the clinical note (or once it has automatically been created for you), you can begin entering patient records, including case notes, letters, referrals, reports and assessments. Formatting your records is similar to formatting in Microsoft Word, and you can format text and paragraphs, move text, add tables and lines. You can also add images and dynamic terms, as well as select your preferred template.

Updating fees and invoices from clinical notes

For clinical notes attached to an appointment/invoice, you can add fees and edit invoice fee amounts while writing clinical notes by clicking the down arrow next to the invoice number:


You can then make the following changes:

  • Changing the fee amount or details for this appointment: click the Edit (pencil) icon next to the fee and make the changes required;

  • Adding another fee to the invoice for this appointment: click Add Fee, then select the fee that you want to add to the invoice (or add the fee to your Fees List here if it is a new fee) and click Save.

  • Deleting a fee: click the Delete (X) icon next to the fee and confirm that you want to delete the fee.

Click the up arrow next to the invoice number to collapse the view.

Saving and publishing clinical notes

Clinical notes are automatically saved as you type. You can also click Save at the top-right to manually save. Once saved, the status of a clinical note is recorded as Draft.

If your internet connection goes down or becomes very slow, you receive a notification telling you to manually save the note by clicking Save, as automatic saving may be affected.

You can publish a clinical note by clicking the small arrow to the right of the Save button and clicking Publish. Publishing converts dynamic text to the actual words - for example, [Patient given name] [Patient surname] becomes the patient's actual name (e.g. John Smith) when published. Once published, the note cannot be edited, allowing you to lock down the note.

Clicking the triangle next to the save button reveals a drop-down menu with more actions

If needed, you can revert a published clinical note back to Draft status to make changes. To revert a note, click the Revert at the top-right of the published note, then click OK to confirm you want to revert the note to Draft status. Once reverted, you are able to make changes to the note.


You can also print clinical notes or share clinical notes where where appropriate.

Deleting a clinical note

To delete a clinical note (e.g. a case note, clinical report or letter), click the small arrow to the right of the Save button when a note is in Draft status. Select Delete from the drop-down menu and confirm that you want to delete the note. The note is then removed from the clinical note listings down the left-hand side.

You can only delete clinical notes that you own (i.e. notes created by you as opposed to another practitioner).

Publishing a clinical note "locks" the note and prevents it from being edited or deleted. To delete a published note, you must first revert the note back to Draft status.

You can also delete a full patient profile on their General page.

Linking referrals to clinical notes

If a clinical note is not already linked to a referral, from the clinical note, click the Edit icon next to the note title and select the relevant referral. When you save, the referral details are automatically populated for you when you print or preview the note.

Attaching Files to Clinical Notes

You can attach a file to a clinical note by following the steps below:

  1. From the clinical note, click Add Files.

  2. Click Upload Files to select the file(s) from your computer, or click-and-drag the file into the area to upload it. You can upload up to 10 files at a time.

    A pop-up titled "File Upload" with a button labelled "Upload Files"
  3. After uploading a file, it will appear in the File Manager. Click the file to add it as an attachment.

  4. Select Clinical to limit access to the file to the patient's practitioner(s) and users with Clinical Access only. Select General/administrative to allow all users to access the file.


You can email the clinical note by clicking the triangle next to the blue button in the top-right, then selecting Email:


To include the attachment, click Add File in the Attachments section.


You may wish to use secure messaging to send sensitive information instead of email.

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