Aberrant methylation of CpG islands (CGIs) is associated with transcriptional silencing of key tumour suppressor genes in cancer and is a frequent epigenetic event in epithelial ovarian cancer (EOC). The methylation status of 24 CGIs in a retrospective group of 142 EOCs and 16 non-tumour adjacent tissues were analysed using methylation-specific PCR (MSP) and Combined Bisulphite Restriction Analysis (COBRA) methods. CGI methylation of at least one of these loci was a frequent event in both early (78%) and late stage (60%) disease. A group of loci were identified as being methylated in 64% of early stage tumours (CGIs linked to the OPCML, RASSFIA and HIC1genes). The HIC1 CGI was frequently methylated in matched non-tumour adjacent tissues, but not in normal ovarian surface epithelium, potentially representing an early epigenetic event in the carcinogenic process present even before apparent morphological change. Differential methylation hybridisation (DMH) of a 12K CGI microarray using ovarian cell lines identified methylation of a CGI located at the LMX1A gene. This CGI was shown by MSP to be a potential early epigenetic marker methylated in 75% of early stage ovarian tumours. 87.5% of the early stage tumours examined were methylated in at least one of four loci (LMX1A, OPCML, RASSFIA or HIC1). The clinical application of this group of methylated CGIs was examined in matched plasma from chemonaive patients with EOC for similar methylation changes. Methylation of LMX1A was detected in 43.3% of all plasma samples and in 48.2% of those patients with methylated LMXIA in their tumour. When methylation was detected in plasma, it was always detectable in the corresponding tumour. Therefore, detection of LMX1A methylation in plasma has a sensitivity of 48.2% and a specificity of 100%.