Although mutations in the MECP2 gene are associated with many cases of Rett syndrome (RS), the phenotype remains unexplained. At least in the early stages, RS and autism have common features; urinary analysis of autistic children has shown an abnormal profile of excretion of sulphur-containing anions, with high levels of sulphite, sulphate and thiosulphate and low values for thiocyanate ions. These parameters were therefore studied in an RS population. Levels of urinary peptides, protein, cysteine, free sulphate, conjugated sulphate, sulphite, thiosulphate and thiocyanate were determined in female RS patients (n = 21) and in controls (n = 21), using standard methods. The urinary volumes were adjusted to standard creatinine levels (200 nmol/mL). Children with RS had higher urinary peptides and protein excretion. Free sulphate values and total sulphate excretion were higher in RS (P < 0.001) than in controls. Cysteine, sulphite and thiosulphate excretion were elevated (P < 0.001) while thiocyanate excretion was greatly reduced (P < 0.001). These results are consistent with reduced expression or activity of the enzyme rhodanese (thiosulphate cyanide sulphurtransferase). Other mutation(s) in genes involved in metabolism of sulphur anions may also contribute to the RS phenotype.