The discovery of several types of small RNAs (sRNAs) has led to a steady increase in available RNA databases. Many of these sRNAs remain to be validated and functionally characterized. Recent advances in microRNA (miRNA)-expression profiling of different tissues, stages of development and physiological or pathological states are beginning to be explored using several technological approaches. In this review, these recent advances in miRNA microarray technology and their applications, particularly in basic research and clinical diagnosis, will be summarized and discussed. The methods for miRNA enrichment and probe design and labeling will also be discussed with an emphasis on evaluation of predicted miRNA sequences, analysis of miRNA expression and exploration of the potential roles of miRNA sequences in the regulation of stem cell differentiation and tissue- and time-specific profiling patterns of their target genes.