Relevance. Targeted sequencing is becoming an increasingly important tool in the diagnosis of infectious diseases in response to the limitations of conventional diagnostic methods and the high cost and complexity of metagenomic sequencing. Aims. To summarize current approaches for targeted next-generation sequencing (tNGS) in infectious disease diagnostics, to highlight its advantages and limitations in comparison with culture-based and PCR-based methods as well as metagenomic sequencing, and to discuss prospects for its implementation in routine clinical practice and genomic surveillance systems. Conclusion. Targeted sequencing has been shown to substantially improve the sensitivity and specificity of pathogen detection while maintaining turnaround time and cost comparable to conventional diagnostic methods. In addition, it enables accurate pathogen typing and the simultaneous generation of data suitable for genomic surveillance and antimicrobial resistance monitoring. Key technological and organizational barriers are discussed, along with future directions in the development of targeted panels and bioinformatic solutions that may establish tNGS as one of the core tools of infectious disease diagnostics in the coming years.