The objective of the present study was to assess the seed health quality, quantification of seed-seedling pathogen transmission and the effect of plant extracts in reducing plant pathogens in the seeds of the tomato varieties San Marzano and Ipa 6. For the seed health, the samples were disinfested, plated and assessed after seven days, according to the Brazilian Seed Analysis Rule. For the transmission rate, 12 trays were prepared with 100 seeds each and assessed at 7, 14 and 21 d.a.s. (days after seeding) using 100 seedlings. The plant (main root, stalk and leaves) tissues were plated in PDA culture medium and assessed after seven days of incubation. Aqueous extracts were prepared from cinnamon, basil, neem and eucalyptus with 0.5% concentration and the seeds were immersed in each solution for 10 minutes. Then, they plated and assessed after seven days. The health test showed that biggest incidences of Aspergillus fumigatus (26 %) and Aspergillus flavus (26 %) were occurred in the seeds of the varieties Ipa 6 and San Marzano, respectively. The fungi A. flavus, A. fumigatus, A. niger, R. stolonifer and Curvularia sp. were detected in quantification of transmission in the seeds of the two tomato varieties. The treatment with basil extract resulted in the least fungus incidence in the transmission quantification of ‘San Marzano’ tomato seeds, while on Ipa 6 seeds the eucalyptus treatment performed better. The interference of treatments was not observed in tomato seed germination. However, there was decrease in incident of pathogens in seeds treated with the plant extracts and different effects was observed based on type and species of the pathogen.