Background: In previous investigations of combined miRNAs/mRNAs expressions in neurodegenerative diseases like Multiple Sclerosis (MS) and Amyotrophic Lateral Sclerosis (ALS) we have targeted some interesting genes and molecular pathways that needed further confirmation. Methods: By nanofluidic qPCR analysis, we aimed to verify the expression of genes that resulted differentially expressed in the previous analyses. Data from MS patients — either the pediatric and the adult occurrence of the disease (adMS and pedMS, respectively) — was compared to age-matched healthy groups. As neurological controls we recruited a cohort of ALS subjects, considering published searches of possible genetic similarities between the two diseases. Results: The main results confirmed the involvement of most of the investigated genes in pedMS and adMS, like BACH2 and MICAL3. On the other hand, suggestive MS candidate genes like TNFSF13B showed an interesting trend possibly influenced by interfering factors, such as concomitant disease-modifying treatments; it is worth noting that TNFSF13B was one of the genes upregulated in ALS compared to age-matched adMS patients, together with the transcription factor TFDP1. Conclusions: Although with caution due to the small sample size, this study confirms the interest in transcriptomic analysis supported by integrated and educated bioinformatics evaluations, to shed further light in complex neurological diseases.