Comparison of methylation patterns in VHL cRCC and sporadic wtVHL cRCC demonstrated that 11 frequently methylated genes (i.e. genes methylated in > 20% of at least one tumour type) were significantly (p < 0.025) more frequently methylated in wtVHL sporadic RCC than in VHL RCC (RASSF1, TWIST1 PITX2, CDH13, HS3ST2, TAL1, WT1, MMP2, DCC, ICA1 and TUSC3:(all p < 0.025; log-likelihood G-test; see Additional file 2). This evidence concerns the gene HS3ST2 and chromophobe renal cell carcinoma.