“One of the most widely-spread of popular superstitions is that relating to stones having a natural perforation. These are everywhere believed to be inimical to all kinds of witchcraft, but more especially are they reckoned as protectors against the much-dreaded yet ever-present Evil Eye.”
The above citation is how Frederick Thomas Elworthy started his short but fascinating paper On Perforated Stone Amulets published in Man (vol 3) in 1903. Most of the stones he discusses were hung outside doors to homes, shops, and animal shelters. As the citation suggests, the stones had natural holes. In the Finnish geology, however, naturally holed stones are very rare. Still, we do have holed stones in the magic object collections. Humans drilled the perforations on these, probably long before their use as magic objects. Thus, we see, for example, spindle whorls and Stone Age clubs among the stone objects in the museums. The people who used them in magic might have found them without knowing who (ancestors, nature spirits, or perhaps God?) made the hole.

When stated in the catalogues, these holed stones have been used in healing, most often by pouring a liquid through the hole to make medicine for constipation or urinary retention, as is the case with other holed objects in the magic collections. The two holed stones (spindle whorls) in the paraphernalia of cunning man Elias Huttunen from Pielavesi include other kinds of use: Huttunen would heal tooth problems by blowing through the hole on the sore tooth or press the stone against rashes or other skin problems.
The holed stones in the Finnish museum collections seem to belong to a different use tradition than the stones Elworthy discussed. Still, evidently there is a shared specialness of the hole. As often is the case when discussing folk religion, the question of why is difficult to answer. One explanation is that perforated stones were more unusual to find than the “normal”, non-perforated ones. Finding a rare object was often seen as a sign from higher powers. We might also look for an answer in human psychology: perhaps the appearance of a hole (nothingness) in an object is a surprising and slightly alarming occurrence? It might be a passage to another reality (otherworld), potentially dangerous if not handled with care?