Infections are the most common causes of tonsillitis. Viral infections cause the majority of sore throats and can do so at any time of the year. Many different viruses may be at fault including rhinoviruses and coronaviruses that cause the common cold, influenza viruses that cause the flu, and Epstein-Barr viruses that cause mononucleosis. However, bacterial infections can also give rise to sore throats, primarily during the winter months. Of these, Streptococcus pyogenes is the most common, especially among children, and results in strep throat. Other bacterial diseases that often cause sore throats are whooping cough and diphtheria. Patients who develop a sore throat after receiving antibiotic treatment or other drugs that affect immune system function may have thrush, a yeast infection of the mouth.

Yet tonsillitis can have other non-infection related causes too. Mild sore throats, especially during the winter when a patient has just woken up, may simply occur because the throat is dry. This can result from the patient breathing very dry air or from breathing through the mouth due to congestion. Similarly, allergies are another frequent sore throat culprit. Allergens may include pollen, mold, pet dander, and dust, and they irritate the back of the throat directly as well as causing congestion that makes patients more likely to breathe dry air in through the mouth.

The throat can also become sore from excessive yelling or irritants such as tobacco smoke, industrial chemicals, spicy food, or alcohol. Acid reflux is another possible cause of sore throats in the morning, as stomach acid is very harsh on the throat. Cuts or other injuries to the back of the throat can also cause soreness and pain. More rarely, a sore throat that lasts for several weeks can indicate a more serious condition such as throat cancer or a compromised immune system as seen in AIDS patients suffering from secondary infections.

While sore throats and tonsillitis have many causes, the patient's other symptoms and medical history often point to a particular possibility. Fortunately, some of these causes, including pollutants, irritating food, and dry air, can be avoided to stop a sore throat throat from worsening or even to prevent it all together. Understanding the root cause of a sore throat will help patients and doctors to develop the most effective treatment and prevention plans possible.