OBJECTIVE To describe the health and wellbeing of alternative education (AE) students from the Northland and Auckland regions of New Zealand and compare these AE students with secondary school students of similar age from the same region. METHODS All 36 AE schools in the region were surveyed in the year 2000. A total of 268 AE students completed a youth health questionnaire using laptop computers. Regional data from a 2001 national secondary school survey that used the same methodology was used for comparison with the AE student data. RESULTS This study found that compared to secondary school students, AE students are more likely to come from disadvantaged backgrounds, with proportionally more AE students reporting socioeconomic difficulty and less parental connection. AE students were more likely to be vulnerable to behaviours that endanger their health, such as drug and alcohol use, risky sexual behaviours and risky motor vehicle use than secondary school students. AE students were also more likely to suffer from high levels of depressive symptoms indicative of significant psychopathology. CONCLUSIONS Findings from this study support the need for specific policies and programs for alternative secondary school students to address urgent and serious threats to their health and wellbeing.