The HSE has said no adult will have to wait more than eight months for an elective procedure, while children will not have to wait more than 20 weeks.
The targets form part of the HSE's National Service Plan for 2013, which details some €721m worth of cuts.
The HSE also said no person would have to wait more than four weeks for an urgent colonoscopy, and that 95% of patients would be admitted or discharged from emergency departments within six hours.
HSE director general designate Tony O'Brien said the organisation was working hard to reduce waiting times across the board.
He said: "Ideally we'd want to get (the waiting period) under 12 to 16 weeks across the board, but with different gradations for those considered urgent and less urgent.
"(This) has been successfully done with symptomatic breast cancer referrals. That has been transformed (under) the national cancer control programme, and similar approaches can work across the system."