A laser capsule marking system and method may comprise at least two indexing wheels, a feeding mechanism, a laser marker, a first inspection system, a rejection subsystem, a reject verification sensor, and a collection device. The wheels are coaxial and have respective circumferential peripheries with multiple open pockets distributed thereabout. Each pocket is configured to releasably receive a pharmaceutical capsule doped with pigment particles reactive to laser light. The indexing wheels are configured to be incrementally rotated in alternating indexing fashion for transporting discrete arrays of respective pockets through a loading zone, an inspection zone, a marking zone, a reject zone, and an unloading zone. An actuatable reject block may be provided to simultaneously blow a rejected capsule from its pocket, and draw it in for transport to a rejection bin. Each circumferential periphery may be comprised of multiple arcuate shoes removably and replaceably secured to their respective indexing wheel.
