It is unclear whether supplemental glutamine is of benefit in haematopoietic stem cell transplantation (HSCT). We performed a systematic review and meta-analyses using Cochrane methodology. Seventeen randomized controlled trials (RCTs) were found. There was considerable heterogeneity between studies in terms of patient demographics and glutamine administration schedule. Many of the studies were small and scored poorly on methodological quality. Oral glutamine may reduce mucositis (average mucositis score: standard mean difference -0.38, 95% confidence interval (CI) -0.59 to -0.16) and days of opioids (mean difference -1.95 days, 95% CI -3.66 to -0.25) and GVHD (relative risk 0.42, 95% CI 0.21-0.85). Glutamine (i.v.) may reduce clinical infections (relative risk 0.75, 95% CI 0.58 to 0.97) and positive cultures (relative risk 0.72, 95% CI 0.57-0.91) but may also increase the risk of relapse (relative risk 2.91, 95% CI 1.34-6.29) but this is based on only two small studies. There was no effect of oral or i.v. glutamine on overall transplant-related mortality at day +100. In conclusion, there may be beneficial effects of glutamine in HSCT but larger, well-designed studies are required to confirm the beneficial effects and investigate possible adverse effects.