The team looked at death rates, weight at birth and pain relief
Researchers have called for an urgent review of the way birth care is delivered in the UK to allow women to make more informed choices.
The team at Dundee University compared births taking place in NHS maternity units with those booked with an independent midwife.
Their study suggests deaths of newborns and stillbirths are more likely in mothers using independent midwives.
However, on a number of other factors, NHS deliveries were poorer.
The researchers studied the cases of 7,214 women who used NHS birth services between 2002 and 2005.
They compared their cases with 1,462 people who had employed a member of the Independent Midwives Association (IMA), now known as Independent Midwives UK.
The researchers said they found important differences between the two groups of women. For example, IMA group mothers were more likely to have a pre-existing medical condition and previous obstetric complications than NHS group mothers.
IMA mothers were also more likely to have a twin pregnancy and breech birth.
IMA mothers were also more likely to experience a stillbirth or a neonatal death than NHS mothers - 1.7% in the IMA group compared with 0.6% in the NHS group.
However, when high risk cases were excluded from both groups, the difference was not statistically significant - 0.5% in the IMA group and 0.3% in the NHS group.
The researchers suggest that it is these higher risk situations, such as breech birth and twin pregnancies, that account for the higher death rate.
On the other hand, the researchers found that IMA mothers were significantly more likely to start labour spontaneously and used fewer pain relieving drugs.
They were also more likely to breastfeed successfully.
Their babies were also heavier. NHS babies were far more likely to be premature and admitted to a neonatal intensive care unit.
The authors said there must now be further study and review so women can make the best decisions about what kind of pregnancy care and delivery they receive.