The aim of this study was to evaluate whether digestive tract mucositis is a predictive factor for body weight (BW) alterations during hematopoietic stem cell transplantation (HSCT). Data about characteristics of transplantation, initial nutritional conditions and gastrointestinal mucositis were collected from adult patients (n = 105) who underwent autologous and allogeneic HSCT. Oral mucositis (OM) was not a predictive factor for BW loss, but it was an independent factor for BW gain in autologous HSCT (β = 0.329, P = 0.021). Busulfan-fludarabine conditioning regimen (β = 1.531, P = 0.011) and gender (β = 1.109, P = 0.038) were significant independent risk factors for BW loss in allogeneic HSCT. Overall survival (OS) was significantly affected by the duration of OM in autologous HSCT (HR = 1.243, P = 0.008). In allogeneic HSCT, BW loss (HR = 1.308, P = 0.049) and diarrhea (HR = 1.139, P = 0.012) interfered significantly with OS. In conclusion, OM was not a risk factor for BW loss, but it influenced BW gain and had a negative impact on OS in autologous HSCT patients. Intestinal mucositis explained partially the BW loss and had a negative impact on OS in allogeneic HSCT.