Methylation of the p16(Ink4a) tumor suppressor gene 5'CpG island was analyzed in 104 primary breast cancer specimens using Southern blotting and methylation specific polymerase chain reaction (PCR) (MSP). Eight and four tumors, respectively, showed methylation, and all MSP positive tumors were detected by Southern blotting. To investigate possible methylation not detectable by these methods, bisulphite genomic sequencing was performed in 220 clones from 14 selected tumors. Absent methylation or methylation of single CpG dinucleotides prevailed in all tumors, but of the MSP positive tumors, three contained alleles with methylation of 31 or 32 of the 32 analyzed CpG dinucleotides in the island. Partially methylated alleles were also observed. In a group with low p16(Ink4a) expression determined by Western blotting, four randomly selected tumors contained several identical clones with methylation of 15 CpG dinucleotides by bisulphite genomic sequencing but with a methylation pattern that did not support detection by either Southern blotting or MSP, increasing the potential significance of p16(Ink4a) methylation in breast cancer.