Under natural conditions, large seeds with physical dormancy (PY) may become water permeable earlier than small ones. However, the mechanism for this difference has not been elucidated. Thus, our aim was to evaluate the traits associated with PY in seeds of Senna multijuga (Fabaceae) and to propose a mechanism for earlier dormancy-break in large than in small seeds. Two seedlots were collected and each separated into large and small seeds. Seed dry mass, water content, thickness of palisade layer in the hilar and distal regions and the ratio between palisade layer thickness (P) in the lens fissure and seed mass (M) were evaluated. Further, the correlation between seed mass and seed dimensions was investigated. Large seeds had higher dry mass and water content than small seeds. The absolute thickness of the palisade layer in the different regions did not show any trend with seed size; however, large seeds had a lower P:M ratio than small seeds. Seed mass correlated positively with all seed dimensions, providing evidence for a substantially higher volume in large seeds. Since wet, but not dry, high temperatures break PY in sensitive seeds of S. multijuga, the data support our prediction that internal pressure potential in the seed and palisade layer thickness in the water gap (lens), which is related to seed mass (i.e. P:M ratio), act together to modulate the second step (dormancy break) of the two-stage sensitivity cycling model for PY break. In which case, large seeds are predetermined to become water-permeable earlier than small ones.