Both cities also rank as having the highest proportion of people with a disability, the latest national snapshot revealed.
Nearly one in five people in Limerick city has a disability while 2.6pc of its residents describe their health as “bad or very bad”.
Cork city dwellers have a disability rate of 17.7pc while 2.2pc say their health status is low, the Central Statistics Office(CSO) revealed.
There is a higher proportion of people with a disability in Waterford city (15.3pc) than in Dublin (14.9pc). But when it comes to bad health Dubliners are ahead at 2pc, compared to 1.9pc in Waterford.
This is the first time in the Census questionnaire that people have been asked to rate their health and is it believed to be a good indicator of the real state of their well-being.
People living in the suburbs of the five major cities had the best overall health.
Disability included sight and deafness problems, intellectual disability, difficulty learning, psychological problems, pain, breathing problems or long-term illness.
The latest snapshot of the nation reveals there is a quiet army of 190,000 people who are providing unpaid care and assistance to families and friends.
They are giving 6.2 million hours of care weekly, an average of 33.6 hours of unpaid help for every carer.
Women, many in their mid to late forties, are providing two-thirds of this form of care.
It also emerged that as many as 4,338 children under 15 years of age are carers.
Overall, there were 595,335 people in the population who had a disability in 2011, a rise of 201,550 over five years.
The report found that widows are more likely to be healthy than separated or divorced people, with married people also found to be healthier than singletons.
There are lower levels of education among the disabled and they are also less likely to have a job. There are 162,681 people with a disability in the labour force, a rate of 30pc compared to 61.9pc for the entire population.
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– Eilish O’Regan Health Correspondent