Sequencing can provide genomic characterisation of specific organism, as well as whole environmental sample. High Throughput Sequencing (HTS) creates an opportunity to generate a huge amount of genomic data at gradually decreasing costs and almost in real-time. HTS is used e.g. in medicine, veterinary, microbiology, virology and epidemiology. The paper presents practical aspects of HTS technology. It describes generations of sequencing, which vary in throughput, read length, accuracy, costs, thus are used for different applications. Several stages of HTS, their aims and pitfalls are presented: extraction of the genetic material, library preparation, sequencing and data processing. For success of whole process all of the stages need to follow strict quality control measurements. Choosing the right sequencing platform, proper sample and library preparation procedures, as well as adequate bioinformatic tools are crucial for high quality results.