To investigate the possible origin of vertebrate asymmetry, we reexamined the long-described asymmetry of pterobranch hemichordates, a group of tiny, mostly colonial marine filter feeders. As first described over a century ago, we found left-right (LR) asymmetry in localization of the gonad. However, contrary to early descriptions, the direction of asymmetry is random, displaying antisymmetry rather than directional asymmetry. We found that the direction of gonad localization is significantly related to the shape of the tube in which the zooid lives. We also reexamined other anatomical features described to have directional asymmetry, the shape of the oral lamella and localization of the gonopore; however, we did not confirm asymmetry in these examples. Together with previous studies, our results suggest that hemichordates have undergone degeneration in the precision of asymmetry from an ancestral asymmetrical condition that existed before the divergence of deuterostomes.