Background: Obesity is a global public health problem. There are a range of treatments available with varying short and long term success rates. One option is the use of anti-obesity medication the prescription of which has increased dramatically in recent years. Despite this, little is known about the individual and GP practice factors that influence the prescription of anti-obesity medication. Methods: Multi-level logistic regression analysis was used to investigate factors associated with the prescription of anti-obesity medication in Northern Ireland using a population primary care prescribing database (~1.5 million people aged 16+ years) during 2009/10. Results: While 25.0% of people are obese, only 1.3% (2.1% of females, 0.6% of males) received anti-obesity medication. The relationship between medication rates and age differed by gender (P < 0.001) with prescriptions higher in younger females and older males. Prescribing of anti-obesity medication reflected obesity prevalence across urban/rural areas and deprivation. There was an unexplained two-fold difference, between the 25th and 75th percentile, in the GP practice prescription of anti-obesity medication. Conclusions: There is evidence of relative under-prescribing in males compared to females despite a similar prevalence of obesity. While the prevalence (and presumably the health consequences) of obesity worsens with age, younger females are more likely to be prescribed anti-obesity medication. This suggests an element of patient demand. Educational material to improve the understanding of the role of anti-obesity medication, for patients and practitioners, is recommended. But further study is needed to understand the factors responsible for the variation in prescribing between GP practices.