Previous studies reported differences in clinical treatments provided to ethnic minority children and white children. We examined whether there were differences in clinical treatments provided to Aboriginal and White infants in Canadian Neonatal Intensive Care Units (NICU) and whether these potential differences could be explained by differences in population characteristics, community size, maternal neighbourhood income and hospital treatment policies. The study population included 10 166 infants (n = 784 Aboriginal and n = 9382 white) admitted to 17 NICUs from all geographical regions of Canada participating in the Canadian Neonatal Network during January 1996-October 1997. We used logistic regression analyses to examine the association between ethnicity and each of seven clinical practices (surfactant treatment, antenatal steroids, blood transfusions, surgery, assisted ventilation, incubator use and transparental nutrition), after adjustment for potential confounders. We repeated theses analyses restricted to infants born <32 weeks gestation. In crude analyses, in the full sample, Aboriginal infants were less likely than white infants to receive surfactants, antenatal steroids, surgery, assisted ventilation, incubator and transparental nutrition. Among infants born <32 weeks gestation, Aboriginal infants were less likely than white infants to receive antenatal steroids, assisted ventilation, incubator and transparental nutrition. In both groups, adjusting for illness severity, gestational age and multiple births separately (model 2) and in combination with neighbourhood income and community size (model 3) resulted in non-significant associations between ethnicity and some of the treatments, but the addition of adjustment for the hospital variation in frequency of use of different treatments resulted in non-significant associations between ethnicity and all seven treatments. Additional studies are needed to explore the significance of hospital frequency of treatment and its relationship to ethnicity.