Knowledge regarding the etiology and prognosis for canine megaesophagus (ME) is currently limited to small case series that may now be out-of-date in light of recent advances in the understanding of neurological syndromes and the availability of advanced diagnostic testing. Ninety-nine dogs diagnosed with non-structural ME were included. Congenital idiopathic ME was present in 10 cases, with complete resolution of clinical signs in only a single case. Eighty-nine cases were considered acquired with most cases being either idiopathic (42.7%) or associated with myasthenia gravis (38.2%). Idiopathic cases represented a smaller percentage of acquired ME than previously reported. Death or euthanasia directly related to ME occurred in almost 50% of acquired cases, whilst clinical signs persisted in around 20% of cases and resolved in 30% of cases. A diagnosis of an underlying etiology, in particular myasthenia gravis, was associated with a better outcome in acquired ME. Megaesophagus continues to be a challenging condition to manage, with a guarded to poor prognosis, particularly when an underlying etiology is not identified. Thorough diagnostic testing for an underlying neurological disorder is important in cases with ME as this may allow institution of appropriate treatment and the potential for a better prognosis.