Introduction: micro-RNAs are small non-coding RNAs capable of regulating the expression level and translation of messenger RNA. Here we compared the microRNA profile of the sinus node in eight week old healthy C57 wild type mice (bl6/j or bl6/n) using either medium-throughput quantitative PCR (qPCR) or next generation sequencing (NGS). Methods: micro-RNAs were measured in liquid N2 snap-frozen SAN tissue. Total RNA was isolated using the miRVana kit in the case of qPCR (Ambion) and the RNeasy Micro kit (Qiagen) in the case of NGS. For the qPCR study, RNA quality was verified using an Agilent 2100 Bioanalyzer, cDNA was generated and preamplified using Megaplex PreAmp Primers Pool A and B and qPCR performed using TaqMan Array Rodent MicroRNA A+B Cards Set v3.0 run on a 7900HT Fast Real-Time PCR System (all reagents and equipment from Applied Biosystems). Data were analysed using RQ manager (Applied Biosystems) and RealTime StatMiner (Integromics) which incorporates a GeNorm stability score algorithm to identify most stable housekeeping genes. Data were calculated as efficiency−ΔCt. In the NGS study, 2 cDNA libraries were prepared from pooled samples from 3 mice using TruSeq Small RNA Sample Prep Kit (Illumina). PCR amplified cDNA libraries were gel purified and 22 nucleotide and 30 nucleotide RNA fragments extracted, purified and validated for size and quality using an Agilent 2100 Bioanalyzer. 50 base pair single-end reads were sequenced using an Illumina MiSeq sequencer. Libraries were aligned to mm10 assembly of mouse genome using Tophat2 and alignments with the best score reported from each read. The mapped reads were then counted against the gtf files obtained from miRbase, mmu.gff3, with HTSeq. These methods were used to retrieve 50 bp single-end reads and up to 3 million total reads enabling identification of ~716 miRNAs. Data are given as DESeq normalised values. Results and Conclusions: Although there were differences between the two studies, for example different methods were used to isolate micro-RNA, the expression of different micro-RNAs should be qualitatively if not quantitatively similar in the two studies. Over 200 micro-RNAs could be unequivocally identified in both data sets and expression as determined by NGS was plotted against expression determined by qPCR. Surprisingly, there was no correlation (e.g. Fig. 1). Many micro-RNAs, abundant as determined by qPCR, were barely detected by NGS. It is concluded that there are major differences in gene expression as determined by qPCR and NGS and these differences need to be understood and resolved.