Abstract Background Examine the onset of a clinical diagnosis of mood (major depression, dysthymia and bipolar disorder)- and anxiety disorders (panic disorder, agoraphobia without panic disorder, social phobia, specific phobia and generalized anxiety disorder) by Body Mass Index levels at baseline in the general adult population over three years. Methods Data are from NEMESIS-2, a representative psychiatric cohort study in the Netherlands. A total of 5303 subjects aged 18–64 were interviewed with the CIDI (3.0 based on DSM-IV) in two waves, with an interval of three years. The first wave was performed from November 2007 to July 2009, the second wave from November 2010 to June 2012. Results Persons with obesity at baseline had a significantly increased risk of the onset of any mood -or anxiety disorder adjusting for covariates compared to persons with a normal Body Mass Index (OR = 1.71; 95% CI: 1.11–2.62). The odds ratio of the underweight category was non-significant. A dose–response effect of the continuous BMI scores on the onset of any mood or anxiety disorder was found (OR = 1.06; 95% CI: 1.02 = 1.10; p < 0.01). Conclusions Obesity at baseline is a risk for the onset of mood -and anxiety disorders at three year follow up.