Advances in next-generation sequencing (NGS) technologies have made the detection of the molecular causes of paediatric diseases increasingly affordable, accessible and rapid. While exome sequencing and genome sequencing were until recently only available for research, they are now used in health care practice. The clinical application of NGS has raised many challenges in genetic counselling for families in terms of the interpretation of test results and incidental findings, as well as technical limitations in the event of inconclusive results. Given the impact of genetic results in clinical decision-making, specialized knowledge is required of the techniques and methods used in genetic studies, their advantages and limitations, and their potential psychosocial, legal and ethical impact on patients, relatives and health care professionals. The ethical implications of parents giving consent to genetic testing in their offspring and the potential disclosure of genetic diseases for which there are limited therapeutic options are still under debate. In this review, we provide an overview of all these aspects, including the advantages and limitations of current NGS techniques, and discuss the possibilities of upcoming solutions.