Acoustic tomography is based on the velocity variation inside the inspected element. However, wood is heterogeneous and anisotropic, which causes natural velocity variations. In wood, the great challenge to apply this technology is to interpret and differentiate the natural variations of the material from those caused by deterioration. This study aimed to evaluate the interference caused by knots, the wave propagation direction, and the effect of juvenile and reaction wood on the velocities determined via ultrasonic tomography. The tests were performed using 40 disks of Pinus elliottii. From the results it was concluded that intrinsic orthotropy of the wood was reflected in the wave propagation on the disks with radial velocities greater than the tangential ones, higher velocities in the knot zones, and different velocities in the zones of compression and opposition wood. In the measurements using the diffraction mesh, the edge velocities (tangential direction with the maximum angle from the radial direction) were always lower than all of the other velocities in the disk. More significant variations in the velocity were obtained in the juvenile wood. These results contribute to quantifying some interferences associated with tomography images, such that the misinterpretation can be minimized.