The Pope underwent a throat operation on Thursday after he was having difficulty breathing.
The Pope is recovering in hospital
The procedure was carried out at Rome's Gemelli Hospital where he had spent 10 days earlier this month with similar flu-related symptoms.
BBC News explains what the procedure, called a tracheotomy, involves.
What is a tracheotomy?
This is a procedure where the surgeon makes a hole in the air passage to allow the patient to breathe.
A tube is passed through the hole, down the throat and into the main airway at the top of the lungs.
The term tracheostomy is sometimes used interchangeably with tracheotomy.
Strictly speaking, however, tracheostomy usually refers to the opening itself while a tracheotomy is the actual incision.
How is it done?
There are two different ways that a tracheotomy can be done, depending on whether it is an emergency or not.
Incision is made in the trachea just below the larynx
A tube is inserted
The tube can be attached to a ventilator
In emergency situations it can be performed quite rapidly by making a cut in a thin part of the voice box or larynx, called the cricothyroid membrane.
A tube is inserted and connected to an oxygen bag. This emergency procedure is sometimes called a cricothyroidotomy.
In the Pope's case, the procedure was carried out under general anaesthesia as a non-emergency and took about 30 minutes.
The incision was made through the skin and the wall of the wind pipe or trachea, just below the larynx.
Why are they done?
Tracheotomies are made for a number of reasons.
They allow nursing staff to keep a patient's airways clear of mucous.
A tracheotomy may also be done if the patient has a swelling in their neck or throat and is having difficulty breathing.
In Pope John Paul II's case, his breathing problems were related to a respiratory infection.
A ventilator can be connected to the tube that goes down the throat to assist breathing.
Being on a ventilator is not as terrible as it sounds.
In some situations, people are awake on ventilators.
Some people say it can be comforting knowing the machine is working for them and that it does not feel as if you are fighting the machine to breathe, as those of us who have not been through this might imagine.
Are there any risks?
Medical experts say a tracheotomy operation is routine, but there is a risk of bleeding and damage to other structures in the neck such as the thyroid gland.
The Pope's procedure went smoothly with no obvious complications, but he is currently unable to talk because of the procedure.
Will the Pope make a complete recovery?
After a nonemergency tracheotomy, the patient usually stays in the hospital for three to five days, unless there are complications or they have other medical problems.
It takes about two weeks to recover fully from the surgery.
The tube can be removed at a later date and the hole will heal. The patient would then go back to breathing normally.
When the Pope regained consciousness he is said to have raised his hand to acknowledge the team of doctors caring for him.
Being an elderly man, aged 84, and in a frail condition, there is a chance that the Pope could develop an infection after such an operation.
And the illness is all the more serious because of his Parkinson's Disease, which may impair his powers of recovery, Rome University neurology professor Giuseppe Bruno told the BBC.
But Peter Simpson, president of the Royal College of Anaesthetists emphasised: "The procedure is routine, safe and one that is done a lot.
"About a third of patients who are on intensive care units for breathing problems will have a tracheotomy.
"People of the Pope's age can get over severe chest infections."