Interstitial Cystitis: This condition is characterized by chronic pelvic pain, pressure, or discomfort related to the bladder, often accompanied by at least one other urinary symptom like persistent urge to void or frequency. The presence of epithelial cells and polymorphs in the urine without a positive culture can suggest an inflammatory process not caused by a typical bacterial infection, making interstitial cystitis a plausible diagnosis.

Viral Cystitis: Some viruses can cause cystitis, and these infections might not be detected by standard urine cultures that are primarily designed to identify bacterial pathogens. The presence of inflammation (indicated by polymorphs) without bacterial growth could suggest a viral etiology.
Fungal Cystitis: Although less common, fungal infections can cause cystitis, especially in immunocompromised patients or those with indwelling catheters. Fungal cultures might be necessary to diagnose these infections, which could explain the negative bacterial culture.
Tuberculous Cystitis: This is a form of extrapulmonary tuberculosis that affects the urinary bladder. It can cause chronic inflammation and might not be detected by routine urine cultures. The presence of sterile pyuria (pus in the urine without bacterial growth) could suggest this diagnosis.

Malignancy: Although rare, bladder cancer or other malignancies affecting the urinary tract can cause symptoms similar to cystitis, including hematuria (blood in the urine) and sterile pyuria. It's crucial to consider and rule out malignancy, especially in patients with risk factors or persistent symptoms.
Stones or Obstruction: Urinary tract stones or obstruction can cause inflammation and infection-like symptoms without a positive culture. These conditions require prompt diagnosis and treatment to prevent complications.
Sexually Transmitted Infections (STIs): Certain STIs, like chlamydia or gonorrhea, can cause cystitis-like symptoms. These infections might not be detected by standard urine cultures and require specific diagnostic tests.

Sarcoidosis: This systemic disease can affect the kidneys and bladder, leading to symptoms that mimic cystitis. It's a rare cause of sterile pyuria and would typically be considered after more common causes have been ruled out.
Chemical Cystitis: Exposure to certain chemicals, such as those used in chemotherapy or as antiseptics, can cause inflammation of the bladder. This diagnosis would be considered in patients with a relevant exposure history.
Eosinophilic Cystitis: A rare condition characterized by the presence of eosinophils in the bladder wall, leading to inflammation and symptoms similar to cystitis. It might be considered in patients with atopic disorders or a history of allergies.