AIM: To analyze differences in prevalence and pattern of tooth agenesis and craniofacial morphology between non syndromic children with tooth agenesis with and without upper cervical spine morphological deviations and to analyze associations between craniofacial morphology and tooth agenesis in the two groups together. METHODS: One hundred and twenty-six pre-orthodontic children with tooth agenesis were divided into two groups with (19 children, mean age 11.9) and without (107 children, mean age 11.4) upper spine morphological deviations. Visual assessment of upper spine morphology and measurements of craniofacial morphology were performed on lateral cephalograms. Tooth agenesis was evaluated from orthopantomograms. RESULTS: No significant differences in tooth agenesis and craniofacial morphology were found between children with and without upper spine morphological deviations (2.2 ± 1.6 vs 1.94 ± 1.2, P > 0.05) but a tendency to a different tooth agenesis pattern were seen in children with morphological deviations in the upper spine. In the total group tooth agenesis was associated with the cranial base angle (n-s-ba, r = 0.23, P < 0.01), jaw angle (ML/RLar, r = 0.19, P < 0.05), mandibular inclination (NSL/ML, r = -0.21, P < 0.05), mandibular prognathia (s-n-pg, r = 0.25, P < 0.01), sagittal jaw relationship (ss-n-pg, r = -0.23, P < 0.5), overjet (r = -0.23, P < 0.05) and overbite (r = -0.25, P < 0.01). CONCLUSION: Etiology of tooth agenesis in children with upper spine morphological deviations was discussed. The results may be valuable for the early diagnosis and treatment planning of non syndromic children with tooth agenesis.