Northland parents declining to immunise their children and "marked socio-economic deprivation" could be behind the region's low vaccination rate, a wide-ranging study has found.

Northland has double the national rate of unimmunised children with 7 per cent not vaccinated at six weeks, according to the study.

Northland medical officer of health Juliet Rumball-Smith led the study that tracked almost all babies born in Northland from 2009 to 2013, 11,972 children, and results were published in the latest issue of the New Zealand Medical Journal.

"We have a high proportion of parents and caregivers who actively refuse immunisation for their babies. The rate of immunisation 'decline' in Northland is more than twice the national average," Dr Rumball-Smith said. "We followed this group of children and found that this decision is long-lasting, as more than 95 per cent of these children go on to be declined subsequent immunisations as well. This has important implications for the health of these children."

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With 41.6 per cent of the children living in "marked socio-economic deprivation" their health could be worsened by exposure to vaccine-preventable illness, the study said.