Diagnosis is achieved mainly by plain and contrasted radiographical and ultrasound imaging. Colonic marker transit studies are useful to distinguish colonic inertia from functional outlet obstruction causes. In this test, the patient swallows a water-soluble bolus of radio-opaque contrast and films are obtained 1, 3 and 5 days later. Patients with colonic inertia show the marker spread throughout the large intestines, while patients with outlet obstruction exhibit slow accumulations of markers in some places. A colonoscopy can also be used to rule out mechanical obstructive causes. Anorectal manometry may help to differentiate acquired from congenital forms. Rectal biopsy is recommended to make a final diagnosis of Hirschsprung disease.

An important distinction in recognizing megaesophagus is the difference between when a dog regurgitates or vomits. When a dog regurgitates there is usually not as much effort involved as when a dog vomits. Often when regurgitating, the dog will tip its head down and the liquid and/or food will almost appear to "spill out" of its throat.

One of the primary dangers to a dog with megaesophagus is aspiration pneumonia. Because the food stays lodged in the throat, it can often be inhaled into the lungs causing aspiration pneumonia. One way to avoid this is to make sure that every time the dog eats or drinks anything, that the dog sits for at least 10 minutes afterwards or is held in a sitting up or begging position. This disorder has a guarded prognosis, however a successful management technique is vertical feeding in a Bailey Chair.

Megaesophagus can also be a symptom of the disease myasthenia gravis. Myasthenia gravis is a neuromuscular disease where the primary symptom is weakness in various body parts of the dog. However, when myasthenia gravis occurs in older dogs it is thought of as an immune-mediated disease. Often when myasthenia gravis is diagnosed in older dogs the first symptom the dog may manifest is megaesophagus.

Myasthenia gravis occurs when acetylcholine receptors (nicotinic acetylcholine receptors) fail to function properly, so that the muslce is not stimulated to contract.

Possible treatments include:

- In stable cases, use of laxatives and bulking agents, as well as modifications in diet and stool habits are effective.

- Corticosteroids and other anti-inflammatory medication is used in toxic megacolon.

- Antibiotics are used for bacterial infections such as oral vancomycin for "Clostridium difficile"

- Disimpaction of feces and decompression using anorectal and nasogastric tubes.

- When megacolon worsens and the conservative measures fail to restore transit, surgery may be necessary.

- Bethanechol can also be used to treat megacolon by means of its direct cholinergic action and its stimulation of muscarinic receptors which bring about a parasympathetic like effect.

There are several surgical approaches to treat megacolon, such as a colectomy (removal of the entire colon) with ileorectal anastomosis (ligation of the remaining ileum and rectum segments), or a total proctocolectomy (removal of colon, sigmoid and rectum) followed by ileostomy or followed by ileoanal anastomosis.

This condition is usually diagnosed by direct examination of the larynx under light sedation, which also allows checking for benign or malignant tumors. Tests, such as thoracic radiographs, CT-scans, or echocardiography, are sometimes needed to rule out heart, lung, or mediastinal diseases or other possible causes of the symptoms often seen with LP. Some vets may also recommend running a thyroid profile since LP can be a symptom or complication of hypothyroidism.

Mild cases are managed by limiting activity, keeping a healthy body weight, and avoiding exposure to high ambient temperatures. Mild sedatives can be used to decrease anxiety and panting and therefore improve respiration. Corticosteroids may also be administered in acute cases to decrease inflammation and edema of the larynx.

Severe acute symptoms, such as difficulty breathing, hyperthermia, or aspiration pneumonia, must be stabilized with sedatives and oxygen therapy and may require steroid or antibiotic medications. Sometimes a tracheotomy is required to allow delivery of oxygen. Once the patient is stabilized, surgical treatment may be beneficial especially when paralysis occurs in both aretynoid cartilages (bilateral paralysis). The surgery (aretynoid lateralization, or a "laryngeal tieback") consists of suturing one of the aretynoid cartilages in a maximally abducted (open) position. This reduces the signs associated with inadequate ventilation (such as exercise intolerance or overheating) but may exacerbate the risk of aspiration and consequent pneumonia. Tying back only one of the aretynoid cartilages instead of both helps reduce the risk of aspiration. Afterwards the dog will still sound hoarse, and will need to be managed in the same way as those with mild cases of LP.

Recent studies have found that many dogs with laryngeal paralysis have decreased motility of their esophagus. Animals with a history of regurgitation or vomiting should be fully evaluated for esophageal or other gastrointestinal disorders. Dogs with megaesophagus or other conditions causing frequent vomiting or regurgitation are at high risk for aspiration pneumonia after laryngeal tie-back. Permanent tracheostomy is an alternative surgical option for these dogs to palliate their clincical signs.

The presence of "T. cruzi" is diagnostic of Chagas disease. It can be detected by microscopic examination of fresh anticoagulated blood, or its buffy coat, for motile parasites; or by preparation of thin and thick blood smears stained with Giemsa, for direct visualization of parasites. Microscopically, "T. cruzi" can be confused with "Trypanosoma rangeli", which is not known to be pathogenic in humans. Isolation of "T. cruzi" can occur by inoculation into mice, by culture in specialized media (for example, NNN, LIT); and by xenodiagnosis, where uninfected Reduviidae bugs are fed on the patient's blood, and their gut contents examined for parasites.

Various immunoassays for "T. cruzi" are available and can be used to distinguish among strains (zymodemes of "T.cruzi" with divergent pathogenicities). These tests include: detecting complement fixation, indirect hemagglutination, indirect fluorescence assays, radioimmunoassays, and ELISA. Alternatively, diagnosis and strain identification can be made using polymerase chain reaction (PCR).

There is currently no vaccine against Chagas disease. Prevention is generally focused on decreasing the numbers of the insect that spreads it ("Triatoma") and decreasing their contact with humans. This is done by using sprays and paints containing insecticides (synthetic pyrethroids), and improving housing and sanitary conditions in rural areas. For urban dwellers, spending vacations and camping out in the wilderness or sleeping at hostels or mud houses in endemic areas can be dangerous; a mosquito net is recommended. Some measures of vector control include:

- A yeast trap can be used for monitoring infestations of certain species of triatomine bugs ("Triatoma sordida", "Triatoma brasiliensis", "Triatoma pseudomaculata", and "Panstrongylus megistus").

- Promising results were gained with the treatment of vector habitats with the fungus "Beauveria bassiana".

- Targeting the symbionts of Triatominae through paratransgenesis can be done.

A number of potential vaccines are currently being tested. Vaccination with "Trypanosoma rangeli" has produced positive results in animal models. More recently, the potential of DNA vaccines for immunotherapy of acute and chronic Chagas disease is being tested by several research groups.

Blood transfusion was formerly the second-most common mode of transmission for Chagas disease, but the development and implementation of blood bank screening tests has dramatically reduced this risk in the 21st century. Blood donations in all endemic Latin American countries undergo Chagas screening, and testing is expanding in countries, such as France, Spain and the United States, that have significant or growing populations of immigrants from endemic areas. In Spain, donors are evaluated with a questionnaire to identify individuals at risk of Chagas exposure for screening tests.

The US FDA has approved two Chagas tests, including one approved in April 2010, and has published guidelines that recommend testing of all donated blood and tissue products. While these tests are not required in US, an estimated 75–90% of the blood supply is currently tested for Chagas, including all units collected by the American Red Cross, which accounts for 40% of the U.S. blood supply. The Chagas Biovigilance Network reports current incidents of Chagas-positive blood products in the United States, as reported by labs using the screening test approved by the FDA in 2007.

If deterioration of the adrenal glands progresses far enough, a dog may experience an Addisonian crisis, an acute episode during which potassium levels increase (hyperkalemia), disrupting normal functions of the heart. Arrhythmia can result and blood pressure may drop to dangerously low levels, while the dog's kidneys may cease to function properly. Some 35% of canine Addison's cases are diagnosed as the result of an Addisonian crisis. It is a medical emergency.

Dogs with infected with the whipworm "Trichuris trichiura" can exhibit low sodium and high potassium values, as is seen in hypoadrenocorticism; however, their ACTH values are normal.