Background Gestational diabetes mellitus (GDM) is a complication of pregnancy that can be associated with neonatal complications and adverse pregnancy outcomes. Recently, probiotic use has been proposed for better control of glucose in GDM patients. The aim of this study was to evaluate the effect of probiotic yoghurt compare with ordinary yoghurt on GDM women. Methods In this double-blind placebo-controlled clinical trial, 84 pregnant women with GDM were randomly assigned into two groups of 42 recipients who underwent 300 g/day of probiotic yoghurt or placebo for 8 weeks. Blood glucose, HbA1c, and the outcome of pregnancy were compared between the two groups after the intervention. Results According to the findings of present trial no significant differences were observed in general characteristics between the two groups (p > 0.05). Both fasting and post prandial blood glucose as well as the level of HbA1c were decreased significantly in probiotic group (p < 0.05), although these changes are not statistically significant in the placebo group. The between group differences was significant after the 2 month intervention (p < 0.05). Neonates born of probiotic group mothers, have significantly lower weight and fewer macrosome neonates were born in this group compared with control group (p < 0.05). However, no difference was observed in other values of outcome. Conclusions Our study revealed that better control of blood glucose can be achieved by consumption of probiotic yoghurt in patients whose pregnancy is complicated by GDM, compared with placebo. Also incidence of macrosomia may be decreased by this regimen.