Abstract Background Gastrointestinal endoscopy plays a crucial role in the diagnosis and management of gastrointestinal disorders. When endoscopy is indicated during pregnancy, concerns about the effects on pregnancy outcome often arise. The aim of this study was to assess whether lower gastrointestinal endoscopies (LGEs) across all three trimesters of pregnancy affects pregnancy outcomes. Methods A systematic literature search was performed using Embase (including MEDLINE), Medline OvidSP, Cochrane Central Register of Controlled Trials, Web-of-Science, Google scholar and Pubmed. All original research articles from 1990 until May 2014 involving pregnant women who underwent LGE for any indication were included. Adverse pregnancy events like spontaneous abortion, preterm birth and fetal demise were assessed for a temporal and etiological relation with the LGE. Results In total, 5514 references were screened by two independent reviewers. Eighty-two references met the inclusion criteria and were selected. Two retrospective, controlled studies, one uncontrolled study and 79 case reports were identified. In the three studies, birth outcomes did not differ between women undergoing LGE during pregnancy, compared to women that had an indication for LGE but in whom LGE was not performed because of pregnancy. In 79 case reports, 92 patients are described who underwent 100 LGE’s during pregnancy. LGEs performed in all trimesters (n = 32, 39 and 29) were both temporally and etiologically related to 1, 3 and 2 adverse events, respectively. Conclusion Based on the available literature, this review concludes that lower gastrointestinal endoscopy during pregnancy is of low risk for mother and child in all three trimesters of pregnancy.