The advance of microfluidics started in the early 1980s. At the time, researchers realized that many processes and reactions in chemistry and biology, which typically take place on small length scales, can be defined, controlled and understood much better when using tools on equally small length scales. Reactions and reaction kinetics rely on (gradual) concentration differences and microfluidics provides the unique possibility to establish exactly such gradients of solutes, ion concentrations, pH value and so on. Nowadays the variety of specific microfluidic methods is large. In principle, they can be divided into two groups: (i) monophase flow, where miscible (e.g. aqueous) fluids are mixed, mostly by diffusion owing to the laminar flow on small length scales and (ii) multiphase flow, the most prominent example of which is probably droplet microfluidics, where water-in-oil or oil-in-water emulsions are used to encapsulate chemical or biological systems and separate them from each other, much like in 'micron-scale test tubes'. Now, 30 years later, microfluidic techniques are seriously considered for industrial applications, although some important steps in the upscaling process are still missing. The purpose of this special issue is to shed light on the different aspects in microfluidics research starting from fundamental research reaching all the way to industrial applications. The study by Toma and co-workers takes advantage of the controlled diffusive mixing when co-flowing aqueous, miscible solutions. They combine microfluidics with optical, spectroscopic and scattering techniques to study DNA packing. Nunes et al review the different regimes when replacing one of the fluids by an oil phase and varying flow rates and device geometries with a particular emphasis on using multiphase microfluidics for synthesis of particles or fibres. Going into the third dimension by fabricating microfluidic devices with several layers, producing emulsions can also be achieved by so-called 'step emulsification', the physical mechanisms behind which are described by Dangla et al. Tran and co-workers move a considerable step towards applicability of water-in-oil emulsions for biological research and review ultrahigh-throughput methods used for bio-assays. The article by Lagus et al focuses this topic specifically on single-cell experiments. Whereas it is very popular to use emulsions with drop sizes of a few tens of micrometers as 'tiny test tubes' they may also serve as templates for materials fabrication. Gundabala and co-workers combine both aspects by producing so-called 'celloidosomes', which consist of liquid drops decorated with yeast cells at the outer interface. Wang et al fabricate microcrawlers that can be thermally set in motion. Finally, Holtze gives a perspective on the possibility to upscale and apply such methods in industry. The choice of papers shows the wide and diverse applicability of microfluidics in various fields of research. While microfluidics started out as a 'niche' technique for very specific applications and as a tool in fundamental soft and biological matter research, the advancements made during recent years promise further progress in the chemical industry, biomedicine and pharmacology. Advantages such as low sample consumption, single cell accessibility and controlled experimental parameters in general may in the future be exploited for real industrial sized applications. In Journal of Physics D: Applied Physics we find a journal that is ideally positioned to give applied microfluidics research a wide readership across many disciplines. In the publication of this special issue we hope to inspire and encourage microfluidics researchers, and to promote interdisciplinary collaborations. We would like to thank all of the authors for their excellent contributions to this special issue.