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Background  Rett syndrome (RTT) is an X-linked neurodevelopmental disease affecting predominantly females caused by  MECP2  mutations. Although RTT is classically considered a monogenic disease, a stable proportion of patients, who do not exhibit  MECP2  sequence variations, does exist. Here, we have attempted at uncovering genetic causes underlying the disorder in mutation-negative cases by whole genome analysis using array comparative genomic hybridization (CGH) and a bioinformatic approach.    Results  Using BAC and oligonucleotide array CGH, 39 patients from RTT Russian cohort (in total, 354 RTT patients), who did not bear intragenic  MECP2  mutations, were studied. Among the individuals studied, 12 patients were those with classic RTT and 27 were those with atypical RTT. We have detected five 99.4 kb deletions in chromosome Xq28 affecting  MECP2  associated with mild manifestations of classic RTT and five deletions encompassing  MECP2  spanning 502.428 kb (three cases), 539.545 kb (one case) and 877.444 kb (one case) associated with mild atypical RTT. A case has demonstrated somatic mosaicism. Regardless of RTT type and deletion size, all the cases exhibited mild phenotypes.    Conclusions  Our data indicate for the first time that no fewer than 25% of RTT cases without detectable  MECP2  mutations are caused by Xq28 microdeletions. Furthermore, Xq28 ( MECP2 ) deletions are likely to cause mild subtypes of the disease, which can manifest as both classical and atypical RTT.