Background: MicroRNAs (miRNAs) are small non-coding RNAs affecting the expression of target genes via translational repression or mRNA degradation mechanisms. With the increasing availability of mRNA and miRNA expression data, it might be possible to assess functional targets using the fact that a miRNA might down-regulate its target mRNAs. In this work we computed the correlation of expression profiles between miRNAs and target mRNAs using the NCI-60 expression data. The aim is to investigate whether the correlations between miRNA and mRNA expression profiles, either positive or negative, can be used to assist the identification of functional miRNA-mRNA relationships. Results: Predicted miRNA-mRNA interactions were taken from TargetScan 4.1 and miRBase release 5. Pearson correlation coefficients between the miRNA and the mRNA expression profiles were computed using NCI-60 data. The correlation coefficients were then subject to the Benjamini and Hochberg correction. Our results show that the percentage of TargetScan-predicted miRNA-mRNA interactions having negative correlation in expression profiles is higher than that of miRBase-predicted pairs. Using the experimentally validated miRNA targets listed in TarBase, genes involved in mRNA degradation show more negative correlations between miRNA and mRNA expression profiles, comparing with genes involved in translational repression. Furthermore, correlation analysis for miRNAs and mRNAs transcribed from the same genes shows that correlations of expression profiles between intronic miRNAs and host genes tend to be positive. Finally we found that a target gene might be down-regulated by more than one miRNAs sharing the same seed region. Conclusion: Our results suggest that expression profiles can be used in the computational identification of functional miRNA-target associations. One can expect a higher chance of finding negatively correlated expression profiles for TargetScan-predicted interactions than for miRBase-predicted ones. With limited experimentally validated miRNA-target interactions, expression profiles can only serve as a supplementary role in finding interactions between miRNAs and mRNAs.