Craniosynostosis (CS) is defined as the premature fusion of cranial sutures, leading to an abnormal skull shape. The overall incidence is between 1: 2,000 and 1: 3,000 live births. Genetic causes are found in 20% of cases. CS can be isolated (non-syndromic CS/NSCS) or they can be part of multiple congenital abnormalities syndromes (syndromic CS/SCS). A few SCS, such as Crouzon, Pfeiffer, Apert and Saethre-Chotzen syndromes, are very well known and their molecular bases have been clarified in the 90s and early 2000s, thus showing the major role of the FGF receptors and TWIST signaling pathways in the etiology of these conditions. The recent availability of powerful molecular tools for genetic diagnosis, such as whole exome or whole genome sequencing, has led to the characterization of the molecular bases of an increasing number of CS, thus emphasizing the significant genetic heterogeneity of these conditions, and blurring the limit between SCS and NSCS. The genetic characterization of patients affected by CS leads to appropriate genetic counseling and provides relevant information concerning comorbidity and prognosis. Nevertheless, this can also lead to the detection of susceptibility factors with low penetrance whose interpretation in genetic counseling is difficult and it raises the question of its cost-effectiveness for health systems. These aspects suggest the need of a patient-tailored clear rationale for performing genetic tests. In this study, we reviewed the main molecular etiologies reported in the last 15 years of either SCS or NSCS, and we propose a systematic multidisciplinary approach as well as a diagnostic flowchart for the genetic evaluation of these patients.