Six vertebrae (one cervical, three articulated thoracic, and two lumbar) and an incomplete thoracic neural spine from a new late Pleistocene site at Anolaima, Cundinamarca, Colombia, are attributed to the extinct gomphothere (Elephantoidea, Proboscidea) Notiomastodon platensis. The preserved bones exhibit a range of alterations, including porosities, piercings, hollows, and deep bone lesions on the spinous process and the neural arch; asymmetrical zygapophyseal articulations; and osteoarthritic lesions. Diet, behaviour, ecological aspects, selective pressures, and disease have the potential to affect the bones, so the study of individual variations and palaeopathology provides important information for understanding aspects of the life of extinct organisms. Osteological anomalies in the Anolaima gomphothere are interpreted as the result of nutritional deficiencies in essential minerals caused by environmental stresses, possibly related to the palaeoenvironmental instability that characterized the late Pleistocene and that coincides with the age of the fossils. Excessive biomechanical loading on already weakened bones from locomotion through the uneven, upland terrain of the Anolaima region may have contributed to the pathologies. This palaeopathological analysis is the first for Colombian megafauna, and thereby broadens our knowledge of the health conditions of South American gomphotheres.