Anorexia nervosa is a serious psychiatric disorder characterized by the inability to maintain normal body weight. The frequently studied polymorphisms in the serotonin 5-HT2A receptor gene (-1438A/G) and in serotonin transporter 5-HTT gene (LPR, VNTR) have led to controversial results in different populations. The aim of the study was to address association of the above-mentioned polymorphisms with anorexia nervosa in the Czech population. We genotyped a well-defined group of 75 patients with anorexia nervosa (average age of 25.39 years, SD 6.18; average BMI 14.65 (SD 1.38)). The control group consisted of 65 Caucasian healthy females (average age 25.76 years, SD 5.12; average BMI 20.69, SD 1.85). The 5-HT2A receptor -1438A/G polymorphism analysis showed a trend for the association with odds ratios for risk allele A being in the same direction. In combination with a previously published Polish cohort, the allelic test reached a suggestive borderline (P = 0.0362, chi2 statistics, 1 df). In meta-analysis which included all published results for allelic tests, the resulting P value was highly significant (0.0003, chi2 statistics, 1 df). Using quantitative association of 5-HTR2A polymorphism with BMI in the Czech sample, a borderline association (P = 0.055) was observed. In 5-HTT, LPR polymorphism analysis, unlike in 5-HT2A, neither allelic nor quantitative association with BMI for the bi-allelic 5-HTT marker was observed. Results of this study support previous reports of a significant role of the A allele (-1438A/G, 5-HT2A receptor) as a risk factor in anorexia nervosa.