Antral pathoses and anatomical variations increase the risk of surgical complications during a lateral window sinus augmentation procedure. Therefore, an understanding of maxillary sinus diseases and anatomies is imperative. In the first part of this article, common sinus diseases will be reviewed, which include acute/chronic rhinosinusitis, mucoceles, pseudocysts, retention cysts, and odontogenic diseases of the maxillary sinus. In addition, a treatment strategy will be proposed toward the management of these antral diseases. In the second part, anatomical variations of the maxillary sinus, for example, the septum and artery that is in approximation to the osteotomy site will be discussed. Knowledge of diagnosing and managing sinus pathoses and anatomies could assist surgeons in reducing the incidence of sinus augmentation complications.