Nicotine increases serotonin release in the brain. Gene polymorphisms in the serotonergic system have been suggested to be associated with smoking behavior. We investigated a possible association between two polymorphisms in the serotonergic system - HTTLPR of a serotonin transporter gene and 5-HT(2A) at position T102C - with biochemical and anthropometric parameters, and with cigarette smoking in an investigation of 200 smokers and 111 non-smokers. The two polymorphisms, HTTLPR and 5-HT(2A) at position T102C, were genotyped by PCR-RFLP. They were not significantly associated with smoking status in these Thai males. Among the smokers, thiocyanate concentrations and quantity of cigarettes smoked (cigarette pack-years) were significantly higher for individuals with LL/LS genotypes than SS genotypes of 5-HTTLPR (all P < 0.05), whereas "age at starting smoking" and "duration of smoking" were not significantly different between these two genotypes. Moreover, anthropometric variables, comprising triceps skinfold thickness, arm circumference, waist circumference, hip circumference, and waist-to-hip ratio, were significantly higher for the CC/TC genotypes of 5-HT(2A) than the TT genotype (all P < 0.05), except for body mass index. HTTLPR and 5-HT(2A) T102C polymorphisms were not significantly associated with smoking status among Thai males; however, the HTTLPR polymorphism among smokers appears to be an indicator of increased smoking intensity consisting of cigarette pack-years and thiocyanate concentrations. The 5-HT(2A) T102C polymorphism plays a role in the anthropometric profiles, triceps skinfold thickness, arm circumference, waist circumference, hip circumference, and waist-to-hip ratio, but not smoking status in Thai subjects.