For bladder cancer, a new diagnostic marker is needed to avoid painful cystoscopy. The aim of this study was to explore the efficacy of urinary miRNA-96 as molecular marker in bladder cancer diagnosis and its relation to bilharziasis. Urine cytology, serologic assessment of schistosomiasis and estimation of miRNA-96 by real-time PCR were carried out for 94 bladder cancer patients, 30 benign bladder lesions and 60 healthy individuals. Expression of miRNA-96 showed a significant difference among the three tested groups and also between benign and malignant bilharzial cases. Urinary miRNA-96 is a good noninvasive diagnostic biomarker for bladder cancer.