Microplastics can be present in the environment as manufactured microplastics (known as primary microplastics) or resulting from the continuous weathering of plastic litter, which yields progressively smaller plastic fragments (known as secondary microplastics). Herein, we discuss the numerous issues associated with the analysis of microplastics, and to a less extent of nanoplastics, in environmental samples (water, sediments, and biological tissues), from their sampling and sample handling to their identification and quantification. The analytical quality control and quality assurance associated with the validation of analytical methods and use of reference materials for the quantification of microplastics are also discussed, as well as the current challenges within this field of research and possible routes to overcome such limitations. Display omitted •Microplastics have been identified as environmental pollutants.•The sampling, sample handling, identification and quantification of microplastics were discussed.•The validation of analytical methods and use of reference materials for the microplastics quantification were highlighted.•The current challenges in these issues are identified.