Age estimation in adults is a complicated task because of various external factors occur concurrently with increasing age. The geometric morphometric method (GMM) is an approach that focuses on shape analysis and is widely recognized for its high reliability and reproducibility. The aim of this study was to explore the variation of cervical vertebrae among different age groups of the Malaysian population by GMM. Lateral skull radiographs of 432 subjects comprising four adult age groups; young adult age group (20–30 years old), early middle age group (31–40 years old), late middle age group (41–50 years old) and, elder adult age group (51–60 years old) were selected. Fifty-three 2-dimensional (2D) landmarks were applied to the digitalized radiographs by TPSDig2 (Version 2.31) software. Geometric morphometric analysis was performed by MorphoJ software. Results showed that the first three principal components (PC) contributed to 47.71 % of the cervical vertebrae variation and were shown in both lollipop and wireframe graphs. Procrustes ANOVA indicated that the shape was significantly different among different age groups. Canonical variate analysis revealed significant differences of both mahalanobis and procrustes distances among age groups with substantial individual overlap within groups. Discriminant function analysis (DFA) showed a correct classification rate for 61.5 % of cases respective to age groups. In conclusion, this study found significant differences in the shape of cervical vertebrae among different age groups of the Malaysian population using the GMM.