Baru fruits from EMBRAPA/CPAC, were collected from different places in the Cerrado region and separeted by matrix. The seeds with healthy aspect were evaluated for seed borne fungi using the following method: blotter test and potato-dextrose-agar medium (PDA). Seeds no healtly and dark from different matrixes, were uniformly mixed in only one sample and evaluated by blotter test. The following fungi were found in seeds: Aspergillus niger, Aspergillus flavus, Aspergillus sp., Penicillium sp., Phomopsis sp., Chaetomium sp., Fusarium oxysporum, Fusarium sp., Rhizopus sp., Pestalotia sp. and Trichoderma sp. The present work showed that the fungi studied were distributed in different intensities between regions and between matrixes from the same region. The darkened seeds of baru evaluated by blotter test presented 62% of Phomopsis sp. In patogenicity tests carried out for Phomopsis sp., in baru seeds, the percentage of emergence seedling was lower in inoculated seed than in non inoculated, producing damping-off and not allowing seedling formation.