Planktic foraminifera (Protista, Rhizaria) are marine zooplankton that precipitate calcareous shells. Their shells are built during their ontogeny, which is characterized by the sequential addition of chambers with various morphology. Here we present computed tomography image stacks of mid-Miocene (Langhian and Serravallian) planktic foraminifera species of Praeorbulina glomerosa circularis, Orbulina suturalis and Velapertina indigena, obtained from sediment and core samples from the Western Carpathians and Pacific Ocean. The X-ray computed tomography scanning was performed with the SkyScan 1172 high-resolution micro-computed tomography device at the Natural Museum in Prague (Czech Republic). The reconstructed 3D models were used to reconstruct the morphological changes accompanied by the species ontogenetic development. In this way we provided new insights into the planktonic foraminifera shell architecture and the three species phylogenetic relatedness.