A HIQA inspection of Our Lady's Children's Hospital in Crumlin has found that all clinical areas examined were generally unclean with the exception of the emergency department.
The Health Information and Quality Authority published 14 hygiene and infection prevention reports.
The findings are highly critical of four hospitals in Dublin, Galway, Limerick and Tipperary.
The reports were highly critical of the Mid-Western Regional Maternity Hospital in Limerick, South Tipperary General in Clonmel, Portiuncula Hospital in Ballinasloe and of Our Lady's Children's Hospital in Crumlin.
Inspectors also reported problems at Connolly Hospital Blanchardstown and the Midland Regional Hospital Portlaoise.
HIQA said that poor hand-washing practice in many Irish hospitals is potentially putting patients at risk of acquiring a hospital infection.
It also said some immediate serious risks to patients were found, with emergency department patients being accommodated with patients with communicable diseases.
A patient with a transmissible disease was in an emergency department cubicle for 30 hours at Connolly Hospital in Dublin.
A similar problem was identified at South Tipperary General.
Unlocked and accessible clinical waste bins were on a thoroughfare for patients at the Mid-Western Maternity Hospital in Limerick.
One of the three clinical areas was unclean at Portiuncula Hospital.
A clinical waste bin was not available in the dirty area at the Midland Regional Hospital in Portlaoise.
The 12 unannounced and two announced inspections, at Connolly Hospital and the Midland Regional Hospital in Portlaoise, found wide variations with regard to hospital cleanliness.
The reports identified problems such as dust and dirt on surfaces, soiled bedpans, worn and damaged furniture, black residue in shower areas, splash marks on equipment and blood stains in various locations.
In some cases, linen and healthcare waste was not being properly managed.
HIQA said the failure to help reduce the spread of infection poses a clear and serious risk to patients.
These are the first HIQA hospital hygiene inspection reports since 2010.
The poorly performing hospitals will be revisited by inspectors within around six months.
Other hospitals can expect inspections over the coming months.