Childhood obesity is associated with psychological problems, but little is known about its association with emotional disturbance (ED) in the educational setting, especially by gender. In the population representative Elementary School Children's Nutrition and Health Survey in Taiwan 2001-2002 of children aged 6-13 (n=2283), we have considered whether ED is associated with obesity by gender. Schoolchildren were assessed with the modified scale for assessing emotional disturbance questionnaires. For some subscales, boys and girls had ED associations with obesity which were bidirectional. With normal weight as referent and relevant adjustments, the significant ED subscales predictable by obesity were relationship problems (RP) in boys (odds ratio, OR=1.89 with 95% CI: 1.08-3.30) and inappropriate behavior (IB) in girls (OR=2.88: 95% CI: 1.47-5.61). Conversely, with 'no-specific-ED' as referent, obesity was predictable by fully-adjusted specific-EDs in the same subscales, namely RP in boys (OR=1.88 with 95% CI: 1.13-3.13) and IB in girls (OR=3.03: 95% CI: 1.57-5.85). Child obesity prevalence showed no trend with school grade from 1 to 6, but for aggregate ED and most of its subscales the prevalence increased with grade (P for trend <0.01). Thus, there is some dissociation of obesity and ED as judged by their trend presence with school grade. Where obesity and ED occurred together (for inability-to-learn and unhappiness or depression), there were upward trends with grade (P<0.01). There are probably some selected bidirectional pathogenicities for obesity-ED associations with different expression in boys and girls and during elementary education. This provides some policy direction while mechanisms and causality require elucidation.