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MicroRNAs (miRNAs) are highly conserved ∼22-mer RNA molecules, encoded by plants and animals that regulate the expression of genes binding to the 3′-UTR of specific target mRNAs or to mRNA itself. The amount of miRNAs in a total RNA sample depends on the recovery efficiency that may be significantly affected by the different purification methods employed. Traditional approaches may be inefficient at recovering small RNAs, and common spectrophotometric determination is not adequate to quantify selectively these low-molecular-weight (LMW) species from total RNA samples. Here, we describe the use of qualitative and quantitative lab-on-a-chip tools for the analysis of these LMW RNA species in plant RNA samples. The same concepts apply to human samples, and our previously published data emphasized the close correlation of LMW RNAs with the expression levels of some human miRNAs. We also applied our result to perform a comparison of some miRNA expression profiles in different tissues. The methods we propose allowed the analysis of the efficiency of extraction protocols, to study the small (but significant) differences among various preparations and to allow a proper comparison of some miRNA expression profiles in various specimens. Therefore, by applying the same concepts and methodologies used for human samples, plant molecular biologists will be able to perform suitable ­comparisons and methodologically correct miRNA expression profiling studies.