Methylation of the Fragile X Related Epigenetic Element 2 (FREE2) located on the exon 1 / intron 1 boundary of the FMR1 gene is related to FMRP expression and cognitive impairment in full mutation (FM - CGG>200) individuals. We examined the relationship between age, the size of the FMR1 CGG expansion and the methylation output ratio (MOR) at 12 CpG sites proximal to the exon 1 / intron 1 boundary using FREE2 MALDI-TOF MS. The patient cohort included 119 males and 368 females, i.e. 121 healthy controls (CGG<40), 176 premutation (CGG 55-170) and 190 FM (CGG 213-2000). For all CpG units examined, FM males showed a significantly elevated MOR compared to that in hypermethylated FM females. In FM males the MOR for most CpG units significantly positively correlated with both age and CGG size (p<0.05). In FM females the skewing towards the unmethylated state was significant for half of the units between birth and puberty (p<0.05). The methylation status of intron 1 CpG10-12 that was most significantly related to cognitive impairment in our earlier study, did not change significantly with age in FM females. These results challenge the concept of FXS related methylation being static over time, and suggest that due to the preference for the unmethylated state in FM females, X-inactivation at this locus is not random. The findings also highlight that the prognostic value of FXS methylation testing is not uniform between all CpG sites, and thus may need to be evaluated on a site by site basis.