Background Autoanalyser methods for the measurement of anti-Müllerian hormone have been introduced into clinical laboratories but few reports of paediatric reference intervals using these new assays have been published. Methods After prior evaluation of the Roche Elecsys anti-Müllerian hormone assay against the Beckman Coulter modified second generation anti-Müllerian Hormone enzyme-linked immunosorbent assay using samples from adult females, a cohort of paediatric samples which had previously been assessed using the Beckman Coulter Access anti-Müllerian hormone assay was analysed using the Roche Elecsys anti-Müllerian hormone assay. Results The Roche Elecsys anti-Müllerian hormone assay measured significantly lower than the Beckman Coulter modified second generation anti-Müllerian Hormone enzyme-linked immunosorbent assay. In the paediatric cohort measured with the Roche Elecsys assay, male levels are very high from birth to puberty after which they fall towards postpubertal female levels. Male results were similar to those previously obtained using the Beckman Coulter Access anti-Müllerian hormone assay on the same cohort. Roche Elecsys anti-Müllerian hormone in the females was very low in the neonatal and prepubertal years and the postpubertal trend, with a steady rise from 15 years, was smoother than previously modelled using the Beckman Coulter Access anti-Müllerian hormone assay. Conclusion Anti-Müllerian hormone levels measured with the Roche Elecsys assay were significantly lower than the Beckman Coulter modified second generation enzyme-linked immunosorbent assay suggesting the need for new reference ranges. In the paediatric cohort, Roche Elecsys anti-Müllerian hormone levels between boys and girls showed good prepubertal delineation and small but statistically significant differences to previously measured levels using the Beckman Coulter Access anti-Müllerian hormone assay on the same sample cohort.