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Objective: To establish a rabbit atrial fibrillation model with rapid atrial pacing (RAP) and investigate its ultrastructural changes and expressions of L-type calcium channel subunits and potassium channel Ky4.3. Methods: Thirty-six rabbits were performed electrical stimulation through bipolar endocardial led by surgical technique, 600 beat per min from 0 to 48 h. Atrial ultrastructure was observed by transmission electron microscope (TEM) after different pacing times. mRNA were measured by reverse transcription-polymerase chain reaction (RT-PCR). Results: Atrial ultrastructure had alteration after 3 hours pacing, such as mitochondria vacuolization, myofilament lysis and glucogen aggregation. The mRNA of the Ca2+ channel β1 and α1 subunits began to decrease after pacing of 6 h, which were paralleled with the change of Kv4.3 mRNA. But the auxiliary subunit α2 were not affected. Conclusion: Ultrastructural changes and mRNA levels of L-type calcium channel subunits and potassium channel Kv4.3 are decreased after RAP, with a mechanism of transcriptional down-regulation of underlying ion channels due to calcium overloading after RAP.