As researchers seek to determine the cellular mechanisms underlying biological processes, they have turned to analyze the functional role of microRNAs to understand this process in details. Here, we investigated the expression pattern of two microRNAs, miR-124 and -134 in maturing neurons and found that the choice of endogenous controls influenced the observed expression levels of these microRNAs. We have cultured rat hippocampal neurons and performed quantitative PCR on the microRNAs using Taqman gene expression assays. The expression of miRNAs was normalised with selected endogenous controls. Using BestKeeper and NormFinder software, we found that 18S rRNA and 5S rRNA to be unsuitable as endogenous controls in this system, while normalising to U6 snRNA produced more consistent results. Our study would like to highlight the importance of empirically testing proposed endogenous controls in any model system before data interpretation is carried out.