The investigation of ultrastructural development and dynamics of thylakoid membranes can provide a valuable information of photosynthetic organism adaptation in relation to environmental factors and stimuli - e.g. ion concentration, illumination or temperature changes. This knowledge, in perspective, can be employed to increase photosynthetic yield and biomass. Structural studies of thylakoid membrane development and their stacking in chloroplast native environment are most typically performed by means of microscopy. Microscopy, however, only allows capturing ’snapshots’ of various dynamical stages. Furthermore, the changes of thylakoid states are of the Ångstrom scale and can appear in a matter of minutes, what makes microscopy analysis a burden. The other common approach - dynamical studies of isolated thylakoid membranes, is sound biochemically, but such studies contain significantly lower structural information, as thylakoid membranes inherently loose their large-scale order upon isolation. Furthermore, thylakoid membrane stacking in vitro is predominantly determined by buffering conditions, therefore an ultrastructural correlation between the thylakoid state in vitro and in vivo is not straightforward. In this PhD work, thylakoid stacking and dynamics is investigated in vivo by means of small-angle scattering and is correlated to the results of microscopy. Measuring small-angle scattering of cyanobacteria, a relative simple unicellular photosynthetic prokaryote, membrane content of which is 90 % thylakoids, enabled formulating a thylakoid form factor, containing a protein-rich membrane separated by two aqueuous compartments, and ultrastructurally arranged as stacked lamellae. This mathematical model has been implemented in the scattering curve-fitting framework ’WillItFit?’, what now enables the fitting of experimental scattering data from photosynthetic organisms. Performing D2O contrast variation study on cyanobacterial cells in vivo strengthens the evidence that scattering peaks origin from both proteins and lipids localized in thylakoid membranes. Fitting this mathematical model to actual SANS scattering curves in their entirety brought the knowledge about cyanobacterial thylakoid membrane and lumen thicknesses, thylakoid-thylakoid repeat distance and related fitting uncertainty parameters (Manuscript 1). This experiment is, up to my knowledge, the first successful mathematical model application, when the entire scattering curve of a complex photosynthetic organismis investigated and system changes are followed in vivo. We are optimistic about, that this scattering model will be applied in investigation of other photosynthetic organisms - both wild-types and functional thylakoid mutants - with the aim to pinpoint the key actors, governing structural thylakoid reorganization and dynamics in their native environments. As an additional experiment, I was able to show that thylakoid repeat distance in wildtype cyanobacteria remains stable upon white light illumination up to 200 μmol photons ·m−2 · s−1 during the 1.5 h measurement timeframe. This result supports two previously published findings, that the dark-light thylakoid dynamics in wild type cyanobacterial cells is lower in comparison to thylakoid dynamics in phycobilisome-deficient mutant strains. Furthermore, I show that cyanobacterial thylakoid ultrastructure is impacted in higher temperatures. Scattering experiments suggest that the average thylakoid repeat distance decreases in 50-60 ° C, but that the overall lamellar thylakoid ultrastructure remains intact, this finding is also confirmed by electron microscopy. I hypothesize that the decrease of thylakoid repeat distance is caused by the increase of hydrophobic interactions between adjacent thylakoid membranes. The knowledge obtained from relatively simple cyanobacterial system has been employed in scattering studies of higher plant thylakoids. I have investigated plants having both the extensive and typical grana systems (Manuscript 2). By extending the methodology of W. Kreutz and W. Menke to SANS experiments on variegated leaves, I have been able to obtain scattering curve of the thylakoid system directly from the plant leaf scattering measurements in vivo and to investigate thylakoid dynamics. Although this work is significantly less progressed in terms of scattering data analysis, by comparing scattering curves from dark-adapted and 500 μmol photons ·m−2 · s−1 white light illuminated plants, I show that shade-tolerant plants having high grana exhibit a smaller light-induced decrease of thylakoid repeat distance than plants with a typical grana-stroma thylakoid ultrastructure. This finding is complemented and supported both by transmission electron microscopy and confocal laser scanning microscopy studies of the same plant species in the same experimental conditions. Overall, the results of this PhD thesis add an important commentary to the ongoing debate, namely that the statement ’lumen contracts/expands upon illumination’ cannot be generalized. In my opinion, lumen behaviour is a secondary effect of the underlying biochemistry (which is barely understood), including ion redistribution, and the statement per se is only scientifically valid if supplemented with plant species, exact experimental conditions and spectral quality, as several outcomes of thylakoid behaviour have been observed - which all can be complementary and not contradictory. In a way, as the author of this PhD thesis has been living in Denmark for some time, he likes to put the following debate in a literature perspective: ’To shrink, or to expand: that is the question’. In my opinion, this biologically important question cannot be justifiably answered unless all biochemical circumstances and actors are known and accounted for. Finally, a small angle neutron scattering study of maize prolamellar bodies is provided. Surprisingly, the intensity of scattering signal was low even in isolated and upconcentrated PLBs in 100% D2O-based buffer, even though the paracrystalline structure of PLB was retained after isolation. Therefore the cubic nature of maize PLBs could not be confirmed by scattering experiments, only by the electron tomography modelling of etioplasts. Importantly, the q position of a single scattering peak from three biological replicates of isolated etioplasts was consistent, which is promising. Scattering signal from PLBs in etiolated leaves in vivo had not been observed, but this ’blank’ experiment made possible to directly subtract the biological background scattering from the Arabidopsis thaliana leaf, which did not otherwise have a scattering measurement of its variegated equivalent. Finally, this thesis contains not only the stepwise mathematical derivation of the necessary mathematical apparatus, but also numerous biological considerations on protein volume fractions in different cellular compartments or issues with scattering length density derivations for a complex biological system - and a thorough discussion on their validity and limitations. For this reason, the first part of the thesis includes a concise X-ray and neutron scattering literature study dating back to 1953 - the very first small angle diffraction measurement of plant chloroplasts’ A critical review on the development of the photosynthetic organism scattering field, together with a more personal reflection on its perspectives is given as a review (Manuscript 3).