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The Desmond Rebellions
According to The Irish History website the Desmond rebellions took an unknown number of lives, but estimated to be "tens of thousands", so I think we can safely say 20,000 at lowest estimate?
The south of Ireland lay devastated, with an unknown number, but certainly tens of thousands dead. The Irish Annals of the Four Masters concluded; At this period it was commonly said, that the lowing of a cow, or the whistle of the ploughboy, could scarcely be heard from Dunquinn to Cashel in Munster”.1 While for the English poet and colonist Edmund Spenser, a most populous and plentiful country was suddenly left void of man or beast”.2
Nine years war
The nine years war was the bloodiest and most brutal of the wars which devastated Ireland during this period. According to The Irish History between 60,000 and 100,000 Irish lives would be a good estimate for having been lost due to famine and war.
theirishhistory.com - counting the cost
How many died between 1594 and 1603? Irish sources claimed that as many as 60,000 people had died in the Ulster famine of 1602-3 alone.[27] Even if this is an exaggeration, counting the unknown number killed in battle or massacred, an Irish death toll of over 100,000 is not excessive. Considering that the population of Ireland at the time was less than 1 million, this means that around one in ten people in Ireland may have died as a result of the war. In addition, thousands of Scottish Gaels fought in the war as mercenaries (mainly, though not only, on the rebel side), several thousand of whom were killed.
English & Welsh casualties
It was apparently not only Irish people that were left devastated by the bloody and brutal war, but at lowest estimate 30,000 English & Welsh lives were also lost.
theirishhistory.com - counting the cost
For the common people of the west of England and Wales, the war was also a tragedy, for it was their sons and husbands who were, mostly unwillingly, conscripted to fight in Ireland. At least 30,000 English & Welsh soldiers died in Ireland in the Nine Years War, mainly from disease. O’Neill himself claimed 70,000, “in action and otherwise”.[28]
What was the likely death toll of the Tudor invasion of ireland?
To avoid controversy or exaggeration I have at every opportunity only went for the lowest estimate, and also only included the major battles and have ignored a few minor incidents along the way that took a few hundred lives here and there at most, and therefore I think it is safe to conclude that at lowest estimate 110,000 English, Welsh and Irish lives were lost during the Tudor conquest of Ireland.
Highest estimate would be above 190,000 people.