Commercial propagation of pequizeiro, which stands out among the main native fruits of the Cerrado region for its high economic potential, has been done by seeds, despite their erratic germination. The objective of this study was to evaluate the effect of seed size and presence of thorns on the endocarp on seedling emergence of pequizeiro in the field. Seeds were collected in a pequizeiro commercial area in Canarana-MT, Brazil. Due to availability, 2,353 thorny seeds (3 sizes) and 106 seeds without thorns (medium sized) were tested. Thorny seeds were classified as large – longer than 50 mm; medium – between 40 and 50 mm; small – less than 40 mm. Seedling emergence started after 50 days in all seed categories, extending up to 100 days in the large seeds and to about 1 year after sowing in the small and medium sized ones. Small seeds showed a lower rate and speed of emergence compared to the others. Large seeds showed higher emergence speed compared to the medium ones. The presence of thorns did not affect seedling emergence. These results indicate the advantages of pequizeiro seed classification for sowing purposes.