Staff and patients from two Brisbane children's hospitals are now under one roof, as the Royal and Mater merge in the new Lady Cilento Children's Hospital.

The difficult job of moving dozens of sick children across Brisbane has wrapped up with the first operational day of the new Lady Cilento Children's Hospital dubbed a success.

Staff and patients from the Mater and Royal Children's hospitals merged on Saturday in the new facility.

Children's Health Queensland (CHQ) Chief executive Peter Steer has praised the efforts of the medical, nursing and ambulance personnel in making the transition.

"We spent the week in both current children's hospitals discharging people as best we could, so that what was left were the children who were quite unwell," Dr Steer said.

He said the patients helped make a tough job easier, saying they, and their parents "have taken a tough journey with a great attitude".

Altogether over an eight-hour period, staff moved 98 very sick children in an operation Dr Steer says has been made easier by learning from recent moves at the Gold Coast Hospital and the Royal Children's Hospital in Melbourne.

"We've had no drama today at all, it has gone exceptionally well," he said.

Lessons learned from Saturday's move will help the new Perth Children's Hospital, which sent observers to witness operations.

The Perth opening is expected 12 months from now.

Dr Steer said Queensland could be proud of its new state-of-the-art children's hospital.

"We can offer every pediatric specialist service similar to any place in the world," he said barring pediatric cardiac transplants, which are only done in Melbourne.

The opening of the new hospital hasn't been without its problems, with a recent Auditor-General's report finding the initial 2006 estimates "significantly underestimated the cost" of delivering the new facility.

AAP.