Caesarean section can result in an indentation of the myometrium at the site of the Caesarean scar, called a niche. Niches can cause symptoms of abnormal uterine blood loss, dysmenorrhoea, chronic pelvic pain and dyspareunia and are possibly related to subfertility. Various other explanations for the cause of subfertility after Caesarean section have been proposed in the literature, such as uterine pathology, intra-abdominal adhesions and women's reproductive choices. Not all niches cause symptoms and the relation with subfertility and a niche in the uterine scar still needs further study since direct evidence is lacking so far. Based on the limited available evidence, and in combination with observations made during sonographic hysteroscopic evaluations and laparoscopic niche repair, we propose and discuss three hypothetical mechanisms: (i) the environment for sperm penetration and implantation may be detrimental; (ii) there could be a physical barrier to embryo transfer and implantation; and (iii) psychogenic factors may reduce the likelihood of pregnancy. Several innovative surgical treatments have been developed and are being implemented for niche-related problems. Promising results are reported, but more evidence is needed before further implementation in daily practice. The additional value of niche resections should be compared to expectant management or fertility therapies, such as ART, in randomized controlled trials. Therefore, our suggested hypotheses should, for the time being, not be used for justification of any specific procedures outside clinical trials.