Multiple myeloma (MM) is a malignancy of plasma cells that not only shows different clinical behavior but also depicts heterogeneous groups at molecular level. The prognosis of the disease has been dramatically changed with the arrival of new drugs in the past few years. In this context of better therapeutic agents, there are important challenges for accurate evaluation of patients by better prognostic and predictive tools. Transcriptomic studies have largely added to decipher MM heterogeneity, dividing MM patients into different subgroups according to prognosis. Micro-arrays and more recently RNA sequencing have helped in evaluating coding and non-coding genes, mutations, unique transcriptome convertors and different splicing events giving new information concerning biology, outcome and treatment options. Initial data from gene expression profiling studies have also pointed out genes that predict prognosis, i.e., CSK1-B, and can deliver pharmacogenomics and biologic vision into the pathophysiology, targeted treatment, and future direction. Importantly, we suggest that all prospective studies and clinical trials now accept genetic testing and risk stratification of MM patients. In this review, we discuss the part and effect of gene expression profiling in myeloma.