Urethral Syndrome: This condition is characterized by dysuria, frequency, and urgency, but with a negative urine culture. It is often caused by urethral irritation or inflammation, which can be due to various factors such as infection with organisms not detected by standard urine cultures (e.g., Chlamydia, Mycoplasma), chemical irritation, or other non-infectious causes.

Vaginitis: In women, vaginitis caused by yeast infections (Candida), bacterial vaginosis, or Trichomonas vaginalis can cause dysuria due to the proximity of the vaginal opening to the urethral meatus, leading to urethral irritation.
Prostatitis: In men, prostatitis can cause dysuria, and the urine culture may be negative if the prostate is the primary site of infection rather than the urinary tract.
Interstitial Cystitis: A condition characterized by chronic inflammation of the bladder wall, leading to symptoms of dysuria, frequency, and urgency without a positive urine culture.

Tuberculosis (TB) of the Urinary Tract: Although rare, TB can infect the urinary tract and cause dysuria. A negative standard urine culture does not rule out TB, as special cultures are required for its diagnosis.
Sexually Transmitted Infections (STIs): Certain STIs like gonorrhea or chlamydia can cause dysuria and may not be detected by a standard urine culture. These infections require specific diagnostic tests.
Kidney Stones: While often associated with hematuria and flank pain, small stones or stones in certain locations might primarily cause dysuria without significant other symptoms.

Bladder Cancer: Rarely, bladder cancer can present with symptoms of dysuria. This would typically be accompanied by other symptoms like hematuria.
Sjögren's Syndrome: An autoimmune disorder that can cause interstitial cystitis and symptoms of dysuria among other systemic symptoms.
Eosinophilic Cystitis: A rare condition characterized by eosinophilic infiltration of the bladder wall, which can cause dysuria and other urinary symptoms.