Mr Kenny said: "There are some moments in history when a seed is sown and the old order changes forever.
"Easter 1916 was such a moment and, from the very early days of this State, it has been the moment we have chosen to commemorate as marking the birth of our sovereign nation."
Relatives of those who died were present as a roll call of the 78 dead, including the 16 executed leaders, was read out by Captain Eoghan Carton and Captain Gillian Costello of the Defence Forces Training Centre.
The rebel chiefs were Roger Casement, Eamonn Ceannt, Thomas Clarke, Cornelius Colbert, James Connollly, Edward Daly, Sean Heuston, Thomas Rice Kent, John MacBride, Sean MacDiarmada, Thomas MacDonagh, Michael Mallin, Michael O'Hanrahan, Patrick Pearse, William Pearse and Joseph Mary Plunkett.
The names of the nationalist volunteers who lost their lives was compiled for the first time with detail on their backgrounds, their addresses, who they fought with, their rank and where and when they died.
From the Irish Citizen Army they were John Francis Adams, Louis Byrne, Philip Clarke, Sean Connolly, James Corcoran, Edward Cosgrave, Charles Darcy, George Geoghegan, James McCormack, John O'Reilly, Thomas Joseph O'Reilly and Frederick Ryan.
From the Irish Volunteers the roll call names Thomas Allen, William Francis Burke, Andrew Joseph Byrne, James Byrne, Charles E Carrigan, Edward Joseph Costello, John Costello, Henry Coyle, John Crenigan, John Cromien, Brendan Donelan, Patrick Doyle, John Dwan, Edward Ennis, Patrick Farrell, James Fox, Sean Howard, Sean Hurley, Cornelius Keating, John Keely, Richard Kent, Gerald Anthony Keogh, Francis Macken, Peter Macken, Michael Malone, Peter Paul Manning, WIlliam McDowell, Charles Monahan, Michael Mulvihill, Richard Murphy, Daniel Joseph Murray, Richard O'Carroll, Patrick O'Connor, Patrick Joseph O'Flanagan, John O'Grady, Michael Joseph O'Rahilly, Richard O'Reilly, John Owens, James Quinn, Thomas Rafferty, George Reynolds, Daniel Sheehan, Patrick Shortis, John Joseph Traynor, Edward Walsh, Philip Walsh, Thomas Joseph Weafer, Patrick Whelan and Peter Wilson.
Only one recorded member of Na Fianna Eireann was on the list - John Healy, a plumber's apprentice, who fought in the GPO and in Phibsborough where he was wounded.
The list was compiled from records in the Military Service Pensions Collection.
Mr Kenny added: "2016 belongs to everyone on this island and to our friends and families overseas.
"It is an invitation to join us in remembering our past, reflecting on our achievements over the last 100 years and to re-imagine our Republic for future generations."
The flags raised were the Irish Citizens Army Flag with the Starry Plough, which was flown from the Imperial Hotel on O'Connell Street, and the Irish Republican Flag and the National Flag, which were both flown from the GPO.
The ceremony, which included military honours and prayer, concluded with the playing of the National Anthem by the Army No 1 Band.
Lord Mayor Criona Ni Dhalaigh and Minister for Arts, Heritage and the Gaeltacht Heather Humphreys were also in attendance.
The military aspects of the ceremony were overseen by Parade Commander Lieutenant Colonel Tim O Brien and Parade Sergeant Major Jim Aherne, both of the 7th Infantry Battalion.
Throughout 2016, more than 40 State ceremonial events will be held as part of the Ireland 2016 Centenary Programme.
One of the highlights will be a major parade through from Dublin Castle to Parnell Square on Easter Sunday.
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