The evolution of borings has shown that the morphology of borings is a function of both the borer and its substrate. This study investigated the effect of bryozoan internal skeletal morphology on the dimensions and distribution of borings. One hundred and forty-three trepostome colonies from the Middle and Upper Ordovician strata of northern Estonia were examined. Of these, 80% were matrix entombed, longitudinally sectioned ramose and hemispherical colonies, and 20% were matrix-free hemispherical colonies that allowed examination of the colony surfaces. Seventy-one percent of the ramose colonies were bored, whereas 88% of the hemispherical colonies were bored. On average, only 8% of colony surface areas were bored out. Borings were more randomly oriented in the hemispherical colonies. In contrast in the ramose colonies, the borings tended to more restricted to the thin-walled endozone and thus parallel to the branch axis. This is interpreted to be a function of the thick-walled exozones controlling to some extent where the borer could bore. Based on morphology, the borings in the hemispherical colonies are referred to Trypanites and those in the ramose colonies to Sanctum. Sanctum is revised to include two possible openings and to recognize that boring shapes were inherently constrained by the thick-walled exozones of the host bryozoan colonies. Both trace fossils were probably produced by a boring polychaete that used the tubes as domiciles.