Many approaches have been applied in biological and clinical studies aimed at simultaneously monitoring the expression of a large number of genes and at identifying the gene expression patterns associated with specific cell types. In the last decade, microarrays are emerged as an innovative tool to detect differentially expressed genes as disease-specific markers and to cluster the co-expressed genes regulating the molecular interactions. In fact, microarrays have been widely used for tumour diagnosis and classification, prediction of prognoses and treatment, pharmaceutical safety assessment, and understanding of molecular mechanisms, biochemical pathways, and gene networks. Besides the clinical relevance and the wide application of this technology, several problems remain to be addressed. This review illustrates the current and future directions of the microarray platform, and highlights the successes and strengths, as well as the shortcomings and limitations of this technology. An overview of microarray impact on the ocular and craniofacial diseases is provided.