The perinatal nutritional environment impacts upon the health and well-being of mother and child also in the long term. The aim of the present study was to determine the safety and efficacy of perinatal probiotic-supplemented dietary counselling by evaluating pregnancy outcome and fetal and infant growth during the 24 months' follow-up. Altogether, 256 women were randomised at their first trimester of pregnancy into a control and a dietary intervention group. The intervention group received intensive dietary counselling provided by a nutritionist and were further randomised, double-blind to receive probiotics (Lactobacillus rhamnosus GG and Bifidobacterium lactis Bb12; diet/probiotics) or placebo (diet/placebo). Firstly, probiotic intervention reduced the frequency of gestational diabetes mellitus (GDM); 13 % (diet/probiotics) v. 36 % (diet/placebo) and 34 % (control); P = 0.003. Secondly, the safety of this approach was attested by normal duration of pregnancies with no adverse events in mothers or children. No significant differences in prenatal or postnatal growth rates among the study groups were detected. Thirdly, distinctive effects of the two interventions were detected; probiotic intervention reduced the risk of GDM and dietary intervention diminished the risk of larger birth size in affected cases; P = 0.035 for birth weight and P = 0.028 for birth length. The results of the present study show that probiotic-supplemented perinatal dietary counselling could be a safe and cost-effective tool in addressing the metabolic epidemic. In view of the fact that birth size is a risk marker for later obesity, the present results are of significance for public health in demonstrating that this risk is modifiable.