Background: Secondary hyperparathyroidism is a well-known complication of end-stage renal disease (ESRD). Both nodular and diffuse parathyroid hyperplasia occur in ESRD patients. However, their distinct molecular mechanisms remain poorly understood. Methods: Parathyroid tissue obtained from ESRD patients who had undergone parathyroidectomy was used for Illumina transcriptome screening and subsequently for discriminatory gene analysis, pathway mapping and gene-annotation enrichment analysis. Results were further validated using RT-qPCR on the independent larger cohort. Results: Microarray screening proved homogeneity of gene transcripts in hemodialysis patients as compared to transplant cohort and primary hyperparathyroidism, therefore further studies were performed in hemodialysis patients only. Enrichment analysis conducted on 485 differentially expressed genes between nodular and diffuse parathyroid hyperplasia revealed highly significant differences in GO terms and the KEGG database in ribosome structure (p=3.70 x 10^-18). Next, RT-qPCR validation of the top differently expressed genes from microarray analysis proved higher expression of RAN guanine nucleotide release factor (RANGRF, p<0.001), calcyclin binding protein (CACYBP, p<0.05) and exocyst complex component 8 (EXOC8, p<0.05) and lower expression of peptidylprolyl cis/trans isomerase and NIMA-interacting 1 (PIN1, p<0.01) mRNA in nodular hyperplasia. Multivariate analysis revealed higher RANGRF and lower PIN1 expression along with parathyroid weight to be associated with nodular hyperplasia. Conclusion: Our study suggests the RANGRF transcript which controls the RNA metabolism to be likely involved in pathways associated with the switch to nodular parathyroid growth. This transcript along with PIN1 transcript which influences the PTH secretion may represent new therapeutical targets to cure secondary hyperparathyroidism.