jats:titleSummary</jats:title>jats:secjats:titleBackground</jats:title>jats:pCone‐beam computed tomography (CBCT) and low‐field magnetic resonance imaging (MRI) are increasingly used in standing horses, so it is important to understand an efficient application of these imaging modalities.</jats:p></jats:sec>jats:secjats:titleObjective</jats:title>jats:pTo compare CBCT and MRI findings in the metacarpo (MCP)/metatarsophalangeal (MTP) region of clinical patients imaged for diagnostic purposes.</jats:p></jats:sec>jats:secjats:titleStudy design</jats:title>jats:pRetrospective study.</jats:p></jats:sec>jats:secjats:titleMethods</jats:title>jats:pThe CBCT and MRI images of the MCP/MTP region from equine clinical patients undergoing both standing MRI and CBCT imaging for lameness localised to the fetlock region (2021–2023) were retrospectively reviewed. Presence, location and imaging features of lesions were compared between modalities using descriptive analysis.</jats:p></jats:sec>jats:secjats:titleResults</jats:title>jats:pImaging studies of 24 MCP/MTP regions from 22 horses were included. CBCT provided the assessment of subchondral bone integrity in palmar/plantar osteochondral disease, details of the length and associated attenuation changes of third metacarpal/tarsal parasagittal groove and proximal phalanx sagittal groove fissures, structural integrity and attenuation changes of subchondral and trabecular bone injuries, proximal phalanx dorsoproximal defects and anatomical and structural details of proximal sesamoid bone injuries. MRI provided the evaluation of short tau inversion recovery (STIR) hyperintensity associated with bone lesions and the extent of increased fluid accumulation in bone. CBCT revealed reduced joint space, indicating articular cartilage loss, while MRI showed joint distension and synovitis. MRI revealed generalised osseous STIR hyperintensity associated with septic arthritis. Soft tissue injuries were most identified by MRI except for heterotopic mineralisation most detected by CBCT.</jats:p></jats:sec>jats:secjats:titleMain limitations</jats:title>jats:pImaging findings not verified by a gold standard.</jats:p></jats:sec>jats:secjats:titleConclusions</jats:title>jats:pCBCT and MRI contributed different diagnostic information so optimal information was obtained by using both modalities. Standing CBCT showed changes in bone structure and attenuation but was limited in detecting soft tissue injuries. Standing MRI showed increased fluid accumulation in bone and soft tissue injuries but was limited in assessing structural details of bone injuries.</jats:p></jats:sec>