Heterogeneity in outcome reporting limits identification of gold-standard treatments for Hirschsprung's Disease(HD) and gastroschisis. This review aimed to identify which outcomes are currently investigated in HD and gastroschisis research so as to counter this heterogeneity through informing development of a core outcome set(COS). Two systematic reviews were conducted. Studies were eligible for inclusion if they compared surgical interventions for primary treatment of HD in review one, and gastroschisis in review two. Studies available only as abstracts were excluded from analysis of reporting transparency. Thirty-five HD studies were eligible for inclusion in the review, and 74 unique outcomes were investigated. The most commonly investigated was faecal incontinence (32 studies, 91%). Seven of the 28 assessed studies (25%) met all criteria for transparent outcome reporting. Thirty gastroschisis studies were eligible for inclusion in the review, and 62 unique outcomes were investigated. The most commonly investigated was length of stay (24 studies, 80%). None of the assessed studies met all criteria for transparent outcome reporting. This review demonstrates that heterogeneity in outcome reporting and a significant risk of reporting bias exist in HD and gastroschisis research. Development of a COS could counter these problems, and the outcome lists developed from this review could be used in that process.