The mouse is a valuable model organism for studying bone biology and for unravelling pathological processes in skeletal disorders. In vivo methods like X-ray analysis, DXA measurements, pQCT and μCT are available to investigate the bone phenotype of mutant mice. However, the descriptive nature of such methods does not provide insights into the cellular and molecular bases of the observed bone alterations. Thus, first-line investigations might be complemented by cell culture-based methods to characterize the pathological processes at the cellular level independent from systemic influences. By combining well-established assays, we designed a comprehensive test system to investigate the cellular and molecular phenotype of primary calvarial osteoblasts in mutant mice compared to wild-type controls as a first-line phenotyping method. The compilation of 9 different quantifiable assays allows assessment of general properties of cell growth and investigation of bone-specific parameters at the functional, protein and RNA level in a kinetic fashion throughout a 3-week culture period, thus maximizing the chance to discover and explain new phenotypes in mutant mice. By analyzing mutant mouse lines for Col1a1 and Jag1 (Delta-Notch pathway) that both showed clear alterations in several bone-related parameters we could demonstrate the usefulness of our cell culture system to discriminate between primary (Col1a1) and secondary effects (Jag1) in osteoblasts.