This study investigated the effects of a maternal dyslipidaemic (DLP) diet on lipid metabolism, microbial counts in faeces and hepatic and intestinal morphology in rat offspring with respect to sex during different phases of life. Wistar rats (dams) were fed a control (CTL) or DLP during gestation and lactation. After weaning, CTL and DLP offspring were fed a standard diet. The effects of a maternal DLP on body composition, biochemical parameters, faecal microbiota and intestinal and hepatic histomorphometric characteristics in rat offspring were evaluated at 30 and 90 d of age. The DLP diet during gestation and lactation caused lower birth weight and a greater weight gain percentage at the end of the 90-d period in both male and female offspring. Female pups from DLP dams had higher liver fat levels compared with CTL (P≤0·001) at 90 d of age. Males from DLP dams had greater visceral fat weight and lower Lactobacillus spp. faecal counts at 90 d of age (P≤0·001) as well as lower faecal fat excretion (P≤0·05) and Bacteroides spp. faecal counts (P≤0·001) at 30 d of age when compared with pups from CTL dams. However, both dams and DLP pups showed damage to intestinal villi. A maternal DLP alters intestinal function and lipid metabolism in a sex-specific manner and is a potential predisposing factor for health complications in offspring from the juvenile period to the adult period.