He opted not to include certain priests, however, including ones who died without being publicly charged.
In a letter, Mr O'Malley said 248 of Boston's priests and two deacons have been accused of child sex abuse since 1950.
But he said he decided against releasing 91 of the names, including priests named in unsubstantiated accusations that never went public.
Each of the 159 names published Thursday has been made public previously, though not necessarily by the archdiocese, the Associated Press reports.
They include still-active priests who were cleared of abuse after being publicly accused.
Mr O'Malley acknowledged that some people may have wanted him to 'go further' and release more names.
But he cited concerns about due process and the damage to the reputations of priests, alive and dead, when accused of decades-old crimes that are difficult to verify.
'In the present environment, a priest who is accused of sexually abusing a minor may never be able to fully restore his reputation, even if cleared after civil or canonical proceedings,' Mr O'Malley said.
'Reputational concerns also become acute in cases concerning deceased priests, who are often accused years after their death with no opportunity to address the accusations against them.'
Mr O'Malley said the archdiocese's effort to compile a single list of accused clerics was a step toward taking responsibility for clergy sex abuse.
A national scandal broke in Boston in 2002 which revealed church leaders had shifted paedophile priests between parishes while hiding their crimes.
'I carry with me every day the pain of the church's failures,' Mr O'Malley said.
Stephen Clifford, who says he was abused by a priest while growing up in Wellesley, said he was pleased the archdiocese was 'letting some more daylight in' but disappointed his abuser, who is dead, wasn't listed.
Mr Clifford never went public with his accusation, which the archdiocese found credible enough to agree to pay for Clifford's therapy, he said.
'I know that they know what this priest did to me,' Mr Clifford said.
'And the fact that he's not on this list really makes me wonder, "Gosh, how many more are there like him that should be on the list, who aren't?"'
Boston has been pressured to publish a list, as other dioceses have, since Mr O'Malley said in a 2009 letter that the archdiocese was considering improving its policy on releasing information about accused clergy.
In recent months, prominent victims' attorney Mitchell Garabedian, and the watchdog group BishopAccountability.org have independently released new names of accused priests, while expressing doubts the archdiocese ever intended to be truly forthcoming.
BishopAccountability.org has estimated at least 350 religious workers in Boston have substantive abuse accusations against them, based on the percentages from other dioceses that have disclosed their number of accused.
Advocates for abuse victims say such public lists ensure that credibly accused priests don't remain active and also provide victims with validation, which is a crucial step toward healing.
They accused Mr O'Malley of inflicting more suffering on victims as months passed with no list.
The Rev. Richard Erikson, outgoing vicar general at the Boston Archdiocese, said the time it took to release the list reflects exhaustive efforts to ensure it was complete, fair and accurate.
David Clohessy of the Survivors Network of those Abused by Priests said the list is woefully inadequate, but 'every scintilla of disclosure' matters, because people will know to beware of the men listed.
'If one kid is kept away from one these priests because of this belated, begrudging and incomplete list, that's still very significant,' he said.