Infectious Mononucleosis: This condition, caused by Epstein-Barr virus (EBV), is a common cause of cobblestoning of the tonsils, especially in adolescents and young adults. The appearance is due to lymphoid hyperplasia and infiltration of the tonsillar tissue.

Streptococcal Pharyngitis: Although more commonly associated with exudative pharyngitis, streptococcal infections can also cause lymphoid hyperplasia leading to a cobblestone appearance.
Recurrent Tonsillitis: Chronic or recurrent tonsillitis can lead to lymphoid hyperplasia and the cobblestone appearance due to repeated infections and inflammation.
Allergic Rhinitis: Postnasal drip from allergic rhinitis can lead to chronic irritation and inflammation of the tonsils, potentially resulting in a cobblestone appearance.

Lymphoma: Although rare, lymphoma (such as Hodgkin lymphoma or non-Hodgkin lymphoma) can present with lymphoid hyperplasia and cobblestoning of the tonsils. Missing this diagnosis could have severe consequences.
AIDS: Acquired Immunodeficiency Syndrome can lead to various opportunistic infections and lymphoid hyperplasia, including cobblestoning of the tonsils. Early diagnosis is crucial for management.
Tuberculosis: In some cases, especially in endemic areas, tuberculosis can affect the tonsils, leading to a cobblestone appearance. It's a critical diagnosis not to miss due to its public health implications and the need for specific treatment.

Sarcoidosis: This autoimmune disease can rarely affect the tonsils, leading to granulomatous inflammation and potentially a cobblestone appearance.
Wegener's Granulomatosis (Granulomatosis with Polyangiitis): A rare autoimmune disorder that can affect various parts of the body, including the tonsils, leading to inflammation and potentially cobblestoning.
Kawasaki Disease: Although primarily affecting children and causing vasculitis, Kawasaki disease can lead to lymphoid hyperplasia and potentially a cobblestone appearance of the tonsils in rare cases.