Most sources agree that the epidemic killed about eleven thousand three hundred people out of a population of about sixty thousand to seventy thousand.

The Order's archives record only eight thousand seven hundred and twenty-six deaths, while other sources give the death toll as eight thousand seven hundred and thirty-two. Others estimate it to have been between eleven thousand and twelve thousand.

This death toll makes the epidemic Malta's deadliest plague outbreak

About nine thousand of the twenty-two thousand people living in cities die in the epidemic, amounting to forty-one percent of the population.

Of these, at least two thousand and fifty-seven die in Valletta, eighteen hundred and eighty-five in Senglea, seventeen hundred and ninety in Birgu and thirteen hundred and twenty in Cospicua.

Some sources give higher death tolls of four thousand, two thousand, eighteen hundred and fifteen hundred respectively for these four cities.

In the rural settlements, about two thousand of some twenty-nine thousand people die, or six point nine percent of the population (one source gives a death toll of only two hundred).

These include three hundred and nine deaths in Qormi, two hundred and seventy in Żabbar, one hundred and sixty-nine in Żebbuġ and eighty-eight in Rabat.

Among the clergy, the dead include a Knight Grand Cross, eight other knights, ten parish priests, one canon, ninety-five other priests and thirty-four monks.

Ten physicians, sixteen surgeons and over one thousand hospital attendants also die in the plague.