Organoids represent the first in vitro cell culture systems that closely resemble native tissues in terms of cellular composition, architecture and key aspects of physiology. Through the discovery of these cultures, researchers could demonstrate that stem cells retain in vitro their innate tendency to self-organize, thus giving rise to complex structures resembling functioning tissues. Until now, most organoid systems have been obtained relying on ill-defined and clinically irrelevant 3D matrices, in which these organoids are homogeneously exposed to biomolecules that induce in vitro development. However, tissue growth and specification in vivo is a tightly orchestrated process, where a multitude of effectors are presented to the developing tissue spatiotemporally. Thus, even though stem and progenitor cells are able to self-organize to striking extents, there is an imminent need to establish new technologies to control the growth of these self-organizing, organ-mimicking structures. The few already described dynamic culture systems, such as gradient generators, will have to be considerably revisited to accommodate the final size and the extended culture time of these developing in vitro tissues. Considering these limitations, we introduce two innovative technologies that provide the expected flexibility to adapt to organoid cultures and that offer control on morphogenesis in vitro. First, we established a unique method to generate microfluidic networks inside naturally derived and synthetic hydrogels. Using short-pulsed lasers, perfusable microchannels can be fabricated in any transparent matrix. This technique has several advantages over conventional microfabrication approaches, as microchannels can be easily fabricated a posteriori in 3D cell-laden hydrogels. In addition, the resulting microfluidic network can be varied on demand depending on cellular growth and morphogenetic events, without impairing cell viability. Next, in order to control organoids better, a versatile hydrogel-based microwell platform harboring U-shaped microcavities of any size or shape was developed. A wide range of cell types can be readily aggregated into highly homogenous cellular clusters. The differentiation of retinal organoids can be improved by optimizing the culture substrate in combination with a specific medium formulation, giving rise to more photoreceptors. Furthermore, the novel technology was used to reduce the variability and improve the traceability of current organoid cultures grown in 3D matrices. For example, aggregation of low numbers of intestinal stem cells instead of single cells resulted in more homogenous organoid formation. The improved homogeneity allows for non-biased analyses at single organoid levels. Finally, new methods were explored to facilitate the application of these next-generation organoid cultures in pharmacological screenings. Using intestinal organoids derived from a murine disease model of cystic fibrosis, a new label-free method was introduced to precisely read out transepithelial fluid exchanges. By measuring changes in the local molecular density within the organoid lumen, key functional metrics representing transepithelial fluxes could be measured. Taken together, this thesis introduces cutting-edge technologies that offer the possibility to exert control over in vitro organoid development and should therefore facilitate the translation of organoid technology towards pharmaceutical and clinical applications.