BackgroundData regarding the lesion detection ability of different radiotracers are lacking in equine bone scintigraphy.MethodsIn this prospective study, hydroxymethylene diphosphonate (HMDP) and methylene diphosphonate (MDP) were compared in horses with increased radiopharmaceutical uptake either in the caudal cervical region (CS group) or in the proximal metacarpal/metatarsal region (PMR group). Region of interest analysis was used to determine normal bone‐to‐soft tissue ratios, lesion‐to‐normal bone ratios and lesion‐to‐soft tissue ratios. Qualitative scoring and total count rates were recorded for each image.ResultsA total of 213 scintigrams were included. Within the PMR group, there were significantly higher lesion‐to‐normal bone ratios for MDP compared with HMDP (p = 0.02). In the CS group, normal bone‐to‐soft tissue ratios were significantly higher for HMDP (p = 0.01). The interobserver agreement with regard to the qualitative assessment of the scintigrams was poor.LimitationPaired studies, comparing the different radiotracers in the same patient, were not feasible.ConclusionThis study revealed minor differences between the two radiotracers, although these have no practical implications. Both radiopharmaceuticals are well suited for detecting lesions at the investigated sites using equine bone scintigraphy.