Periodontal diseases occur frequently in equine dentistry and excessive strain in biological tissues is assumed to be a predisposing factor in their development. Finite element (FE) analysis enables strains and stresses occurring in the periodontium to be calculated and is a useful tool for testing this hypothesis. The current study aimed to establish reliable 3-D models from equine maxillary and mandibular cheek teeth for use in FE simulations, with particular attention to the detailed construction of the periodontal ligament (PDL). Age-related morphological aspects of the teeth and the periodontium were also considered by constructing different models for three defined age groups. Finally, the biomechanical behaviour of the equine PDL was examined during experimental tooth intrusion (i.e. axial displacement of the tooth into its alveolar socket). The results showed an increase in intrusion with increasing age due to age-related changes in the periodontal elastic properties. The general stress level in PDL and surrounding bone also increased with age. Reliable FE models were established to calculate aetiologically relevant biomechanical effects occurring in the equine periodontium.