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<b><i>Background:</i></b> Different drug dependencies may have unique genetic vulnerabilities. Changes in serotonin availability and function have been linked to addiction. We investigated whether 2 serotonergic polymorphisms, <i>TPH1 A218C</i> (rs1800532) and <i>5-HTT</i>-linked promoter region <i>(5-HTTLPR)</i> (rs25531), are differently associated with alcohol or opiate dependence. <b><i>Methods:</i></b> Alcohol-dependent patients (n = 292), opiate-dependent patients (n = 309), and healthy controls (n = 301) were recruited from the Han Chinese population in Taiwan. Genotypes of <i>TPH1 A218C</i> and <i>5-HTTLPR</i> polymorphisms were analyzed using a polymerase chain reaction with restriction fragment length polymorphism. <b><i>Results:</i></b> The genotype frequencies of the <i>TPH1 A218C</i> polymorphisms were not significantly different in the 3 groups. The genotype frequencies of the<i> 5-HTTLPR S+</i> (<i>S/S</i>,<i> S/L</i>_<i>G</i>,<i> L</i>_<i>G</i><i>/L</i>_<i>G</i>) polymorphisms were significantly higher in opiate-dependent patients (&#x03C7;² = 8.77, p = 0.01), but not after controlling for the covariates of age, gender, and interaction effect in logistic regression analysis. Moreover, there was a significant interaction between the <i>TPH1 A218C A/C</i> and <i>5-HTTLPR S+</i> gene polymorphisms in opiate-dependent (OR 2.72, p = 0.01), but not in alcohol-dependent patients. <b><i>Conclusions:</i></b> Our data suggested that there may be a differential genetic vulnerability in serotonergic genes for alcohol and opiate addiction. However, replications of our findings are still needed.