Value of the data •The meta-analysis performed in this study provides a differential reference expression value for 24,699 known, mapped transcripts, common to total and histologically normal thyroid adjacent to papillary thyroid carcinoma, and a view of the genomic regions with altered expression by a chromosomal segment representation. •The histologically normal thyroid adjacent to papillary thyroid carcinoma is often used as normal control in thyroid tumor studies. Differentially expressed genes identified in this comparison provide a molecular view of the behavior of normal tissue adjacent to papillary thyroid carcinoma vs. total normal thyroid tissue and might yield biological insight about the biology of thyroid tumors. •Enrichment function analysis performed for the gene groups classified on their gene expression ratio intervals identified interesting molecular functions of genes which are under-expressed in total normal thyroid and on the contrary have a high expression level in the normal thyroid adjacent to papillary thyroid carcinoma. •The housekeeping gene search useful for gene expression studies on thyroid tissue retrieved 414 loci, different from those retrieved in the total normal thyroid except for seven genes as ACTG1, BLOC1S2, DIABLO, OCIAD2, GTPBP6, EIF2B2, AKR1B1. •The quantitative reference values of the enzyme mRNAs might be used in metabolic network models for the validation of hypotheses about the relationships among mRNA levels, corresponding enzymatic proteins and the quantities of their substrates or products obtained by metabolome experiments.