microRNAs (miRNAs) are approximately 22nt RNAs that regulate target gene expression. Altered expression of miRNAs has been demonstrated in many different human cancers. Many studies using microarray technologies to characterize miRNA expression profiles have relied on fresh tissue to determine the miRNA signatures. In this study, we prepared total RNA from paired samples of formalin-fixed paraffin-embedded (FFPE) and fresh frozen malignant melanoma, and used that in microarray experiments to compare miRNA expression profiles between FFPE and fresh tissue with corresponding mRNA expression profiles from the same tissue sources. We demonstrate that miRNA expression profile from FFPE tissues closely resembles that from fresh tissues, and the correlation is significantly better than that for mRNA profiles from FFPE and fresh tissues. These results underscore the suitability of FFPE tissues as appropriate resources for molecular expression analyses and support the notion that miRNAs are more vigorous analytes for this purpose than mRNAs.