Calcium phosphates (CaPs) are extensively used as biomaterials for bone repair and regeneration and are considered an interesting synthetic alternative for natural bone grafts. However, the bone regenerative potential of many CaP bone graft substitutes requires further improvements. The bioactivity of CaPs is regulated by a variety of properties, including their chemical composition and (surface) structural properties. In this study, we performed a comprehensive characterization of six CaP ceramics that had been previously tested in a number of in vitro and in vivo studies. The numerical parameters obtained from this characterization were correlated with osteogenesis-associated gene expression and pathways of osteoblastic MG-63 cells cultured on these six materials. The results showed, among others, the influence of structural parameters of the ceramics on cytoskeleton- and extracellular matrix-related gene expression and the influence of both chemical and structural parameters on osteogenesis-associated pathways. The bioinformatics approach presented here allows exploring the transcriptional landscape induced by CaP ceramics and gaining fundamental knowledge about cell-biomaterial interactions.