In previous studies we identified a subset of downregulated serum microRNAs (miRNAs) in familial and a majority (60%) of sporadic ALS patients that was already evident in pre-clinical mutation carriers. A common 5-nucleotide-sequence motif (GDCGG; D = G, A or U) was highly significantly enriched in the downregulated miRNAs indicating the deregulation/malfunction of one or several specific RNA-binding protein(s). Using miRNA-pulldown assays in lysates of HEK293 cells followed by mass spectrometric identification and quantification of precipitated proteins, we identified 37 proteins specifically associated with the GDCGG-motif. Direct and specific binding to miRNAs with the GDCGG-motif of two of the top candidate proteins, FXR1 and FXR2, was confirmed by biochemical assays. Binding domains could be mapped to the RGG-domain of FXR1 and the second RG-domain of FXR2. The third member of the Fragile-X-related protein family, FMRP, causes Fragile-X mental retardation when absent and has already been implicated in ALS pathology. Although not a top candidate protein in our miRNA-pulldown assays, we show direct and specific binding of FMRP to miRNAs with the GDCGG-motif via its RGG-domain highly homologous to the RGG/RG-domains of FXR1 and FXR2, respectively. In vitro binding studies on a transcriptome-wide scale using miRNA-arrays identified the member of the FragileX-related protein family most likely responsible for altered miRNA-profiles in ALS and expression analysis and neuropathological studies will be employed to validate its role in ALS pathogenesis.