Background: Schools are often identified as a site for intervention to improve the diets of students, and help prevent excess weight gain and obesity. Rates of overweight and obesity amongst school children have risen in much of the world, including New Zealand, with unequal distribution by ethnicity and socioeconomic status. Objective: To identify barriers to improving school food environments and promoting healthy nutrition experienced by primary schools in New Zealand. Methods: Five primary schools (ages 5-10 or 5-12 years) were recruited within Wellington, New Zealand. Data included: interviews with school management; school food policy documents; school lunch/food sales; and location of food outlets and outdoor food advertisements surrounding the schools. A case-comparison approach identified barriers to promoting healthy nutrition within primary schools in New Zealand. Results: Common barriers in all schools included the high proportion of food brought to school from home, the crowded curriculum and limited resources to implement changes. Barriers that varied across socioeconomic contexts included the ability of home and community settings to support healthy diets, the degree to which schools relied on fundraising, and engagement of parents and families with the school food environment. Conclusion: New Zealand primary schools face a number of barriers to promoting healthy nutrition related to time and resource constraints, with limited influence on children's diets in relation to home and community settings. Incremental actions to improve school food environments seem most effective, supported by external agency expertise. The nature of external support should to be tailored to the needs of the individual school. (Contains 2 tables.)