OBJECTIVE To conduct a systematic review of studies on early probiotic supplementation to prevent childhood metabolic syndrome (MS). METHODS Using the Cochrane systematic review strategy we searched PubMed, EMBASE, CENTRAL, CINAHL, and the conference proceedings of the Pediatric American Society meetings and trial registries in December 2014. Randomised controlled trials (RCTs) and non RCTs of probiotic supplementation to the mother and/or infant for a minimum duration of 4 wk were selected. Of these, studies that reported on MS or its components (obesity, raised blood pressure, hyperglycemia, dyslipidemia) in children between 2-19 years were to be eligible for inclusion in the review. Risk of bias (ROB) in selected RCTs and quality assessment of non-RCT studies were to be assessed by the Cochrane ROB assessment table and New Castle Ottawa scale. RESULTS There were no studies on early probiotic administration for prevention of childhood MS (CMS). Follow up studies of two placebo controlled RCTs (n = 233) reported on the effects of early probiotics on one or more components of MS in children aged 2-19 years. Meta-analysis of those two studies could not be performed due to differences in the patient population, type of outcomes studied and the timing of their assessment. Assessment of childhood metabolic outcomes was not the primary objective of these studies. The first study that assessed the effects of prenatal and postnatal supplementation of Lactobacillus rhamnosus GG on body mass index till 10 years, did not report a significant benefit. In the second study, Lactobacillus paracasei 19 was supplemented to healthy term infants from 4-13 mo. No significant effect on body mass index, body composition or metabolic markers was detected. CONCLUSIONS Current evidence on early probiotic administration to prevent CMS is inadequate. Gaps in knowledge need to be addressed before large RCTs can be planned.