Congenital anomalies of kidney and urinary tract (CAKUT) represent spectrum of developmental defects, which occur in approximately 1:500 liveborn children and are the most common cause of pediatric end-stage renal disease. The genetic and phenotypic heterogeneity, incomplete genetic penetrance and multifactorial nature of CAKUT creates difficulties in defining the genetic architecture of the disease. The genetic cause of most CAKUT cases remains unknown, therefore the novel approaches in searching for the common disease denominators are required. We have been validated previously assigned genes and identified novel most dysregulated genes in CAKUT by microarray gene expression profiling. Using bioinformatic analyses, we have identified key biological processes and molecular functions enriched in differentially expressed genes (DEGs) in CAKUT. Major molecular networks associated with disorders and molecular pathways in CAKUT were also described. Data from the whole genome expression were also used for the bioinformatic prediction of miRNA activity in CAKUT. Experimental validation of expression of miRNAs identified by the integrative approach revealed that hsa-miR-144, first time identified to be dysregulated in CAKUT, could be connected with biological processes crucial for normal development of kidney and urinary tract.