Objectives: In the present study, it is described the phenotypical analysis and the mutational screening, for genes PAX9 and MSX1, of six families affected by severe forms of tooth agenesis associated with other dental anomalies and systemic entities. Study Design: Six families affected by severe tooth agenesis associated with other dental anomalies and systemic entities were included. Oral exploration, radiological examination, medical antecedents consideration and mutational screening for PAX9 and MSX1 were carried out. Results: No mutations were discovered despite the fact that numerous teeth were missing. An important phenotypical variability was observed within the probands, not being possible to establish a parallelism with the patterns associated to previously described PAX9 and MSX1 mutations. Conclusions: These results bring us to conclude that probably other genes can determine phenotypical patterns of dental agenesis in the families studied, different than the ones described in the mutations of PAX9 and MSX1. Moreover, epigenetic factors can be involved, as those that can reduce gene dosage and other post-transcriptional modulation agents, causing dental agenesis associated or not with systemic anomalies.