Abstract Introduction Evaluating genetic/genomic applications (GGAs) is crucial for their implementation in clinical practice but hindered by several issues, such as rapid development processes and unclear benefits. Since these challenges lack comprehensive discussion, this study aims to identify and analyze all barriers emerged in the Health Technology Assessment (HTA) of genetic/genomic tests, filling a gap in the current literature. Methods PubMed, Scopus and Web of Science were searched to identify studies that specifically discussed any challenge or barrier in the HTA evaluation of GGAs. No restriction was applied on evaluation aspect or study type. Challenges/barriers were then grouped into the domains outlined in the EUnetHTA Core Model. A narrative synthesis of the main findings was performed. This study was supported by the EC and MUR- PNRR-M4C2-I1.3 Project PE_00000019 ‘HEAL ITALIA’. Results 19 articles were included: one third involved experts from different countries, and about 50% were author perspectives. Articles either focused on one aspect only (37%) or were more general (47%). The most challenging domain was economic aspects (69%), followed by clinical effectiveness (47%) and social impact (42%), but issues were found in all domains. The lack of a standardized HTA approach, the paucity of evidence on clinical outcomes, the challenges in capturing all health benefits, and the difficulties in identifying the healthcare pathways triggered by the test were consistently mentioned across the HTA domains. Conclusions Our study systematically summarized challenges in the HTA evaluation of GGAS, providing a thorough analysis and categorization of these issues. Various challenges surfaced, notably related to the identification of costs, as well as clinical and non-clinical benefits. There is a need for exhaustive discussion on potential solutions to facilitate the assessment process of these technologies to ultimately foster their implementation in clinical practice. Key messages • There are multiple challenges in the HTA evaluation of genetic and genomic tests in clinical practice that impact every HTA domain. • There is a need for concrete efforts in generating further evidence in relation to the definition of costs and benefits of the healthcare pathways triggered by genetic/genomic applications.