To evaluate the effect of flavin-containing monooxygenase 3 (FMO3) genotype and dietary choline supplementation on trimethylamine (TMA) metabolism in HyLine Brown laying hens, a 3 × 2 two-factorial arrangement was employed with FMO3 genotypes (AA, AT, and TT) and dietary choline supplemental levels (370 and 2,960 mg/kg of diet) as main effects. At 46 wk of age, 108 hens of AT genotype and 108 hens of TT genotype were randomly allotted to one of the 2 dietary treatments, and each dietary treatment consisted of 6 replicates with 9 birds each. A total of 24 hens with AA genotype was allotted to one of the 2 dietary treatments that consisted of 6 replicates with 2 hens. Hens were fed the diet with 370 mg/kg of choline supplementation for 1 wk of adaptation followed by a 6-wk trial period. Yolk TMA concentration was increased by dietary supplemental choline at 2,960 mg/kg (P < 0.05), and TT hens showed a higher TMA content in egg yolks than that in AA and AT hens (P < 0.05). Dietary supplementation of choline at 2,960 mg/kg increased the TMA concentration of cecal chyme (P < 0.05) and serum (P < 0.05). Hepatic FMO3 mRNA levels in hens were reduced by higher choline added to the diet (P < 0.05). The TMA and methimazole oxidation rate in AA hens was higher than those in AT and TT hens (P < 0.05). A higher choline diet decreased hepatic FMO3 activity by 33.99% (P < 0.05) and 61.39% (P < 0.05) toward TMA and methimazole, respectively. These results suggest that lower hepatic FMO3 activity caused by the mutation may be responsible for the genotype difference in the TMA metabolism. Exposure to a high dosage of dietary choline increased TMA synthesis in the cecum, suppressed activity of FMO3 in liver, and consequently aggravated the burden of TMA metabolism, especially in TT hens.