Aim: The aim of this study was to describe the characteristics at enrolment of children and adolescents referred to an obesity programme and to determine how the prevalence of comorbidities differed in Indigenous versus non-Indigenous children.Methods: Participants were residents of a semi-rural region of New Zealand (NZ). Eligibility was defined by a body mass index (BMI) of ≥98th percentile or >91st centile with weight-related comorbidities. Fasting blood, medical and physical assessments were obtained.Results: During the recruitment period from January 2012 to August 2014, 239 participants, aged 4.8-16.8 years, undertook assessment. Average BMI standard deviation score was 3.09 (standard deviation (SD) = 0.60, range 1.52-5.34 SD). The majority of participants were of either Maori (NZ's indigenous people (45%)) or NZ European (45%) ethnicity; 29% of participants were from the most deprived quintile of household deprivation. Maori participants were more likely than NZ Europeans to have a mother who smoked during pregnancy (52% vs. 28%, P = 0.001), a family history of type 2 diabetes (66% vs. 53%, P = 0.04), acanthosis nigricans on examination (58% vs. 20%, P < 0.0001), a low serum high-density lipoprotein cholesterol (27% vs. 14%, P = 0.03) or high serum triglyceride (38% vs. 24%, P = 0.03) concentration.Conclusion: The unique aspect of this study was the ability to recruit high levels of Maori participants and those from most deprived areas, indicating a high level of acceptability for these target groups. Comorbidities were prevalent in this cohort of overweight/obese school-aged children. While there were some differences in comorbidity prevalence between Maori and NZ Europeans, the overall clinical picture in our cohort, irrespective of ethnicity, was of concern.