In a previous paper (Shtober-Zisu et al., 2012) we described millimeter to centime-sized fluid-free holes within the interiors of stalagmites of widely varying origin. We present here further observations of this phenomenon, using X-ray tomography, macroscopic and microscopic observation of sections of twenty-six stalagmites from various sites in North America and the Caribbean region. We can distinguish three types of cavities in speleothems: primary µm-sized fluid inclusions; mm to cm sized holes, aligned along the stalagmite growth axis which are clearly syngenetic; and µm to cm-sized holes away from the growth axis (“off-axis holes or OAHs”) deeply buried inside their host stalagmites, and cutting primary growth layers. Neither axial nor off axis holes contain fluid today. Off-axis holes appear to have been formed by internal corrosion of the calcite host, possibly enhanced by the action of bacteria which were sustained by permeation of through the body of the stalagmite of water containing dissolved organic species. A modern stalagmite from Israel is shown to contain bacteria associated with active hole formation.