Background Bladder carcinoma is the 2nd most common genito-urinary malignancy in men above the age 40years worldwide and the most common malignancy in men in Sokoto with a prevalence of19.3%. The commonest histopathological type worldwide is transitional cell carcinoma but in Sokoto the predominant histopathological type is squamous cell carcinoma due to endemicity of schistosomiasis. Early diagnosis of bladder carcinoma is still a great challenge. About 70% of our patients present with advanced tumours for which only palliative treatment can be offered. The main stay of screening, diagnosis and follow-up of patients with bladder carcinoma are urine cytology and cystoscopy (± biospsy). Cystoscopy is invasive and costly while urine cytology is poorly sensitive. Therefore there need for effective, non-invasive tool for screening, diagnosis and surveillance of patients with bladder carcinoma. Urinary molecular markers yielded encouraging results in previous studies. This study was on “effectiveness of urinary molecular markers (Bladder Tumour Antigen {BTA} and Survivin) in diagnosis of bladder carcinoma”. It was undertaken to compare the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of Survivin, BTA, and urine cytology in diagnosis of bladder carcinoma and to find out the histopathological types of bladder carcinoma in Usmanu Danfodiyo University Teaching Hospital (UDUTH), Sokoto. Materials and methods It was a 12 –month (January to December 2014) hospital- based prospective cross sectional study of consecutive patients who presented to UDUTH, Sokoto with features of bladder carcinoma. Data were collected via a pro forma that included clinical features, radiologic findings, laboratory results, urine cytology, cystoscopy, bladder tissue histology, BTA TRAK and Survivin Enzyme Linked Immunosorbent Assay (ELISA) findings. Data were analysed using Statistical Package for Social Sciences (SPSS) 20.0 version (2011) for windows. Results A total number of 88 patients participated in the study with 52 in the study group and 36 in the control group. The age range of patients in the study group was (20-78) years with a mean age of 47.17 ± 17.00 years while the age of control group ranged between 18-86 years with a mean age of 44.19 ± 18.89 years. There were 48 males and 4 females in the study group, giving a male:female ratio of 12:1. Thirty-one (60 %) of the patients were farmers and 44 patients (85%) had history suggestive of schistosomiasis at childhood. The sensitivity of urine cytology, BTA TRAK and Survivin ELISA in the study were 29.1%, 98.8%, and 98.8% respectively. The specificity of urine cytology, BTA TRAK and Survivin ELISA were 95.5%, 13.6% and 4.5% respectively (p= 0.05). The PPV of urine cytology, BTA TRAK and Survivin ELISA in the study were 96.2%, 81.7% and 80.2% respectively. The NPVs were 25.0%, 75.0% and 50.0% for urine cytology, BTA TRAK and Survivin ELISA respectively. Using receiver operating characteristic (ROC) curve, appropriate cut off values of the markers was determined with sensitivity and specificity ranges of 97.4- 100.0% and 90.0%- 100.0% respectively. The histopathological types of bladder carcinoma were squamous cell carcinoma (SCC) in 25 patients (59.5%), transitional cell carcinoma (TCC) in 16 patients (38.1%) and adenocarcinoma in 1 patient (2.4%). There was positive correlation between the mean concentrations of the BTA and Survivin with stage and grade of the bladder carcinoma respectively. The markers (BTA and Survivin) were associated with 100% false positive (FP) results in patients with haematuria from other urologic conditions and in patients with benign prostatic hyperplasia (BPH). Conclusion Urinary molecular markers (BTA and Survivin) are highly sensitive (98.9%) and effective in the diagnosis of bladder carcinoma. Survivin and BTA correlated positively with grade and stage of bladder carcinoma respectively. The markers were 100% False Positive (FP) in patients with haematuria from other urologic diseases and in patients with benign prostatic hyperplasia (BPH). The commonest histopathological type of bladder carcinoma was SCC (59.5%). Other histopathological types were TCC (38.1%) and adenocarcinoma (2.4%)