Rett syndrome (RTT) is a neurodevelopmental disorder that almost exclusively affects girls. Recently mutations in MECP2, that encodes the methyl CpG binding protein 2 (MeCP2), have been found to cause RTT. MeCP2 has a role in gene silencing. It binds to methylated cytosine in the DNA and recruits histone deacetylases. We studied the methylation pattern of the promoters of two X chromosomal genes, G6 PD and SYBL1, in patients with RTT and in a control group. Both genes undergo X inactivation which correlates with promoter methylation. A 1 : 1 ratio of methylated versus non-methylated alleles was expected. In the control group a median ratio of 47 : 53 of methylated to non-methylated alleles was found at the G6 PD promoter locus. In 22 patients with RTT the median ratio was significantly different, 33 : 67 (p < 0.0001). Analysis of the SYBL1 promoter revealed an almost identical median ratio of methylated versus non-methylated alleles (RTT 47 : 53; control 49 : 51), however, the range was wider in the RTT group (RTT 23 : 77 to 56 : 44; control 43 : 57 to 55 : 45). There was no apparent correlation between G6 PD promoter methylation status and mutations in the MeCP2 gene or the severity of the clinical phenotype in our patient group. The finding of reduced methylation at the G6 PD promoter is an interesting finding and suggests that there could be widespread dysregulation of X chromosomal genes in Rett syndrome.