Transgenic Bt cotton expresses the Cry1Ac protein from Bacillus thuringiensis, which could influence the plant\'s capability to host endophytic fungi. The diversity of endophytic fungi in leaves, stems and roots from transgenic (Bt) and its isoline (non-Bt) cotton was evaluated during different plant developmental stages to investigate possible non-target effects of genetically modified cotton on endophytic fungal communities. A total of 17 genera of endophytic fungi were isolated. The most frequently isolated species were Phomopsis archeri from leaves and stems and Phoma destructiva from roots. While the Bt modification had no effect on endophytes, the cotton tissue and the plant developmental stage significantly influenced the diversity and composition of the fungal community. These results represent the first evaluation of the composition of endophytic fungi associated with transgenic cotton plants