Sub-millimetre-sized phosphatic spherules are often found in acetic acid-insoluble residues produced for microfossil extraction. As they are typically associated with conodont elements and have a similar chemical composition, they are informally known as ‘conodont pearls’. Still, the origin of these micro-spherules has been controversial, and authors have disagreed regarding their mode of formation, or if they are biogenic or not. In this study, an assortment of micro-spherules from several localities and stratigraphical levels were analysed using multiple methods, in an effort to shed light on the origin of these enigmatic objects: ocular investigation with a stereomicroscope, chemical analyses employing energy-dispersive mass spectrometry, imaging through scanning electron microscope, and synchrotron radiation X-ray tomographic microscopy. Collectively, the techniques employed allow for near-complete characterization and description of the study specimens. At least five different groups, or morphotypes, of spherules can be discerned, which differ both in morphological and chemical details. Most specimens are notably spherical and display concentric layers of growth. Several of the specimens have a central nucleus, sometimes with one or more objects located closely together. Internal details and chemistry suggest that the phosphatic spherules probably are of different origin. Thus, the term ‘conodont pearl’ encompasses confusingly similar objects deriving from different organisms and/or processes, and only careful analysis can reveal their individual origin. The only organisms unequivocally associated with (in situ) phosphatic micro-spherules are ceramoporid bryozoans, and the conodonts Cordylodus and Westergaardodina, but the possible function and significance of these objects remain enigmatic.