a-GvHD may complicate allogeneic HSCT. In this retrospective single-center study, we evaluated incidence and risk factors of a-GvHD in 197 consecutive allogeneic pediatric HSCTs applying Glucksberg and NIH a-GvHD classifications. Among 179 eligible transplants, the cumulative incidence of grade 0-I a-GvHD was 48% and grade II-IV was 52%. None of the considered variables significantly influenced the incidence of grade II-IV a-GvHD. Malignancy and myeloablation were associated with an increased risk of classic a-GvHD (p < 0.01). Seventy-two percentage of children are alive, with a significant difference in OS and TRM between grade 0 and I vs. grade II and IV a-GvHD; this observation was reproduced in the non-malignant setting, while only a disparity in TRM was evidenced in children with malignancy. In our experience, the incidence of a-GvHD was similar, regardless of donor type. Myeloablation and malignant disease represented the only risk factors for classic a-GvHD. Our results highlight the need for a better prevention of this complication in the non-malignant setting.