Risperidone is an atypical antipsychotic agent with efficacy for both positive and negative symptoms of schizophrenia. Risperidone is a potent dopamine D3 antagonist and agonism at D3 sites induces behavioral suppression in rodents. We thus hypothesized that D3 antagonism may contribute to response to risperidone in negative symptoms. This study aimed to explore the influence of the Ser9Gly polymorphism of the dopamine D3 receptor (DRD3) gene on response to risperidone after controlling for nongenetic factors. One hundred twenty-three Han Chinese patients with acutely exacerbated schizophrenia were given risperidone monotherapy for up to 42 days. Clinical manifestations were measured biweekly with Positive and Negative Syndrome Scale and Nurses' Observation Scale for Inpatients Evaluation (for assessment of social functioning). For adjusting the within-subject dependence over repeated assessments, multiple linear regression with generalized estimating equation methods was used to analyze the effects of Ser9Gly polymorphism and other covariates on clinical performance. Compared with patients with the Gly9Gly genotype, those with either Ser9Ser or Ser9Gly had better performance on negative symptoms after control for other prognostic factors (P = 0.0002 and 0.0092, respectively). Patients with the Ser9Ser genotype had better social functioning than those with Gly9Gly (P = 0.0029). The Ser9Gly polymorphism, however, did not significantly affect positive symptoms. Male gender, fewer previous hospitalizations, and higher risperidone dose also predicted better treatment response. These data suggest that the DRD3 Ser9Gly polymorphism or, alternatively, another genetic variation that is in linkage disequilibrium, may influence response to risperidone in negative symptoms and social functioning.