cDNA microarray technology is widely used in various biological and medical disciplines to determine gene expression profiles. Unfortunately, this technology requires a large quantity of input RNA. Since there is an increasing need to more precisely analyze defined cell sub-populations with low cell counts, working protocols using a minimal number of input cells are needed. Optimal RNA isolation and its accurate amplification are crucial to the success of these protocols. The HL60 cell line was used in the search for a suitable protocol that can be used for clinical samples of CD34+ hematopoietic cells obtained from bone marrow. The goal was to discover the best method of isolating and amplifying RNA from a small number of cells. Our evaluation of various methods and kits available in the market revealed that the combination of RNAqueous Kit (Ambion, USA) for RNA isolation and the SenseAmp Plus Kit (Genisphere, USA) for one-round RNA amplification produced the best results. This article presents a verified protocol describing a reliable and reproducible method for producing enough input RNA for microarray experiments when the number of cells is limited.