Aflatoxins are carcinogenic secondary metabolites frequently detected in food and feed stuff based on maize and other crops susceptible to infection with the fungal pathogen Aspergillus flavus. We investigated the metabolization of aflatoxins in chickens by analyzing excreta and ileal content and developed and validated a biomarker method for detection of aflatoxins and their metabolites in these matrices. Analysis of ileal content served to distinguish between urinary and fecal excretion combined in the excreta samples. During a 3-wk animal trial, one hundred sixty-eight 1-day-old chicks were randomly allocated to 24 pens with 7 chicks per pen and subjected to different feed regimens with: A) toxin-free feed, B) feed supplemented with 18 ng of total aflatoxins/g, and C) feed supplemented with 515 ng of total aflatoxins/g. Chicken excreta and ileal content were sampled after 7, 14, and 21 D. An analytical method based on liquid chromatography coupled to tandem mass spectrometry was validated for the determination of aflatoxin B1, B2, G1, G2, M1, P1, Q1, and aflatoxin B1-N7-guanine (AFB1-N7-Gua) in chicken's samples. Comparing chicken excreta, which contain urine and feces, to ileal content, which contains no urine, we explored the secretion pathway of aflatoxin metabolites. The AFB1-N7-Gua was only detected in excreta, whereas aflatoxin M1 (AFM1) was detected both in ileal content and excreta. Aflatoxin M1 was detected in excreta in concentrations 5 times higher than in ileal content, suggesting primary excretion via urine. Although chickens are relatively resistant to aflatoxins, contamination of feed can lead to adverse effects and thus economic losses in farming. Therefore, a biomarker method to estimate the exposure of chickens to aflatoxins can play an important role to monitor the animals' health.