Background: MicroRNAs (miRNAs) are a class of small RNAs that regulate gene expression.They are aberrantly expressed in many human cancers and are potential therapeutic targets and molecular biomarkers. Methods: In this study, we for the first time validated the reported data on the entire set of published differential miRNAs (102 in total) through a series of transcriptome-wide experiments. We have conducted genome-wide miRNA profiling in 17 urothelial carcinoma bladder tissues and in nine normal urothelial mucosa samples using three methods: (1) An Illumina HT-12 microarray hybridization (MA) analysis (2) a suppression-subtractive hybridization (SSH) assay followed by deep sequencing (DS) and (3) DS alone. Results: We show that DS data correlate with previously published information in 87% of cases, whereas MA and SSH data have far smaller correlations with the published information (6 and 9% of cases, respectively). qRT-PCR tests confirmed reliability of the DS data. Conclusions: Based on our data, MA and SSH data appear to be inadequate for studying differential miRNA expression in the bladder. Impact: We report the first comprehensive validated database of miRNA markers of human bladder cancer. © 2013 Zabolotneva, Zhavoronkov, Shegay, Gaifullin, Alekseev, Roumiantsev, Garazha, Kovalchuk, Aravin and Buzdin.