Patulin is a common fungal contaminant of ripe apples used for the production of apple juice concentrates and it is also present in other fruits, vegetables and food products. Patulin is a secondary metabolite produced by species of the genera Penicillium, Aspergillus and Byssochlamys. Patulin has been reported to be mutagenic, carcinogenic and teratogenic. Antigen-presenting cells (APCs) are of prime importance in the innate immune response; they capture antigen in tissues and then migrate to the lymphoid organs to present the antigen to T lymphocytes. Thus, they are crucial for the initiation of immunity. Interdigitating dendritic cells (IDCs) are a subset of APCs that are present at the lymphatic organs. In the thymus, they act in positive and negative selection during T cell development. In the present study, patulin was administered orally to growing male rats aged 5-6 weeks. A dose of 0.1 mg kg(-1) bw day(-1) was given to rats for a period of 60 or 90 days daily. The effect of patulin on the IDCs of thymus was investigated by transmission electron microscopy (TEM), and the results were evaluated in terms of cell destruction. In the rats of the control group, it was observed that the IDCs had an indented nucleus, a clear cytoplasm and numerous membrane extensions. In the cytoplasm, a well-developed golgi complex, mitochondria, granular endoplasmic reticulum and a small number of lysosomal structures were observed. At day 60 of patulin-treated rat groups (P-60), loss of cristae in mitochondria and chromatin margination and lysis in the nucleus were found. It was observed that the IDCs had a perinuclear area of cytoplasm surrounded by a peripheral electron-lucent zone. In the cytoplasm of the 90-day patulin-treated rat group (P-90), a peripheral electron-lucent zone was also found, similar to the P-60 group. Additionally increase in vesicular and lysosomal structures, increase in apoptotic bodies and condensation of chromatin in the nucleus were noted. It was observed that patulin leads to apoptotic body formation and cell apoptosis in the IDCs of rat thymus especially in the P-90-treated groups. Copyright (c) 2007 John Wiley & Sons, Ltd.