Body mass index (BMI) is commonly used as an indicator of obesity, although in both clinical and research settings the use of bioelectric impedance analysis (BIA) is commonplace. The purpose of this study was to examine the relationship between BMI, BIA and percentage body fat to determine whether either is a superior indicator of obesity in men with schizophrenia. The reference method of deuterium dilution was used to measure total body water and, subsequently, percentage body fat in 31 men with schizophrenia. Comparisons with the classification of body fat using BMI and BIA were made. The correlation between percentage body fat and BMI was 0.64 whereas the correlation between percentage body fat and BIA was 0.90. The sensitivity and specificity in distinguishing between obese and overweight participants was 0.55 and 0.80 for BMI and 0.86 and 0.75 for BIA. BIA proved to be a better indicator of obesity than BMI. BMI misclassified a large proportion of men with schizophrenia as overweight when they had excess adiposity of sufficient magnitude to be considered as obese. Because of the widespread use of BMI as an indicator of obesity among people with schizophrenia, the level of obesity among men with schizophrenia may be in excess of that previously indicated.