Housekeeping, or reference genes (RGs) are, by definition, loci with stable expression profiles that are widely used as internal controls to normalize mRNA levels. However, due to specific events, such as pathological changes, or technical procedures, their expression might be altered, failing to fulfil critical normalization pre-requisites. To identify RG genes suitable as internal controls in human non-cancerous kidney tissue, we selected 18 RG candidates based on previous data and screen them in 30 expression datasets (>800 patients), including our own, publicly available or provided by independent groups. Datasets included specimens from patients with hypertensive and diabetic nephropathy, Fabry disease, focal segmental glomerulosclerosis, IgA nephropathy, membranous nephropathy, and minimal change disease. We examined both microdissected and whole section-based datasets. Expression variability of 4 candidate genes (YWHAZ, SLC4A1AP, RPS13 and ACTB) was further examined by qPCR in biopsies from patients with hypertensive nephropathy (n = 11) and healthy controls (n = 5). Only YWHAZ gene expression remained stable in all datasets whereas SLC4A1AP was stable in all but one Fabry dataset. All other RGs were differentially expressed in at least 2 datasets, and in 4.5 datasets on average. No differences in YWHAZ, SLC4A1AP, RPS13 and ACTB gene expression between hypertensive and control biopsies were detected by qPCR. Although RGs suitable to all techniques and tissues are unlikely to exist, our data suggest that in non-cancerous kidney biopsies expression of YWHAZ and SLC4AIAP genes is stable and suitable for normalization purposes.