Statistical analysis of DMRs revealed three novel genes significantly correlated with pre-eclampsia: sorbitol dehydrogenase (<i>SORD</i>, <i>p</i> = 9.98 × 10<sup>-6</sup>), diacylglycerol kinase iota (<i>DGKI</i>, <i>p</i> = 2.52 × 10<sup>-5</sup>), and islet cell autoantigen 1 (<i>ICA1</i>, 7.54 × 10<sup>-3</sup>), demonstrating the potential of WGBS in families for elucidating the role of epigenome in pre-eclampsia and other complex diseases.