Significant gender differences have been described for psychiatric disease prevalence and receipt of psychotropic medication. Second generation antipsychotic (SGAs) drugs are not a homogenous group as they differ in their receptor profiles, clinical efficacy and side effects. Gender differences in pharmacokinetics and side effects of second generation antipsychotic drugs have been investigated in several studies indicating that there is a distinct differences between men and women both for the SGAs as a whole group and for specific drugs in particular. Nevertheless the influence of gender on efficacy and side effects of antipsychotic agents is still not well established. Even though higher rates of side effects are reported in women, recommended pharmacological dosage regimes do not differ between male and female patients. For SGAs, the reasons for a higher risk in females may be multi-causal including gender-related differences in pharmacokinetics, pharmacodynamics, pharmacogenetics, immunological and hormonal factors as well as differences in the use of medications by women compared with men. In this review we give a brief overview of gender-specific pharmacokinetic factors leading probably to distinguished clinical outcome in both sexes. Furthermore the implication of gender on common side effects of SGAs such as weight gain, glucose and lipid abnormalities, hyperprolactinemia, cardiac and sexual side effects is discussed with specific reference to studies done on schizophrenic patients.