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Microfluidics and microtechnologies are of great interest for biological applications. This interest is linked to the fact that microtechnologies enable the study of single cells at the cellular and sub-cellular level. One of many applications of such single cell assays is cell-cell interaction probing. Current cell-cell interaction tools used by biologists rely on manual cell manipulation. But in the last decade new microfluidic technologies have arisen to tackle this biological challenge. Despite this growing need, the developped microfluidic devices still force biologists to compromise between the throughput of the assay (number of cell pairs interrogated) and the control over the interaction parameters (contact force and contact time). This thesis proposes an engineering point of view of microfluidic tools for single cell and in particular cell-cell interaction studies. The developed microfluidic devices enable an advancement of the microfluidic technologies to leverage new tools for cell-cell interaction interrogation in a controlled manner and at a high throughput. In this work we report the development of a novel microfluidic device based on a “roll-over” mechanism. This new chip design enables the multiplexing of cell-cell interactions. This multiplexing is achieved by forcing into contact all cells from a sample of a first cell population with all cells from a sample of a second cell population. Using such a device, we characterized the interaction of cells expressing olfactory receptors. This chip enables the maximization of cell-cell interaction interrogation and thus is ideally suited for rare and nonredundant cell populations. A droplet microfluidic chip for controlled and reliable cell co-encapsulation was designed and implemented. Common droplet microfluidic devices rely either on random cell co-encapsulation in droplets, thus leading to high cell loss, or use multiple microfluidic devices sequentially to perform droplet manipulation steps and achieve cell co-encapsulation. Both cases lead to cell sample loss, first from the random cell co-encapsulation process and second from the possible droplet loss between different microfluidic devices. Therefore, the implementation of a single fully integrated device enabling controlled cell co-encapsulation in droplets is of high interest for the study of precious, large cell libraries interactions for example in the case of cancer immunotherapy. In this thesis we also developed new concepts, using already existing microfluidic designs. By reusing the microfabrication technologies and microfluidic principles of the previously designed devices we could develop a novel microfluidic chip for another biological application. The third device studied in this thesis enables to look further into cell membrane receptors by isolating plasma membrane fragments. This tool enables an in-depth study of receptors involved in cell-cell interactions. It can also be used for any other cell membrane receptor study as for example G protein coupled receptor screening for therapeutic drug discovery. The tools developed in this thesis set the grounds for the development of new generations of cell-cell interaction microfluidic devices, enabling high throughput and control over the cell-cell interaction parameters. The technological advancements presented in this work were validated for various biological applications.