A microscopy system for a thick sample with transverse-illumination of the sample, comprising: - a sample holder; - a detection pathway comprising: - a microscope lens of given optical axis (Δ); - a detection device comprising a detection surface optically conjugate with an object imaging surface in the object space of the microscope lens; - means for relative axial displacement of the microscope lens and of the sample holder; - a sample illumination pathway comprising: - at least one emission source of an illumination beam; - means for forming, from the illumination beam, an illumination surface; - said microscope lens; - deflection means secured to the sample holder making it possible to deflect the illumination surface in the object space at the output of the microscope lens, to form a transverse illumination surface, situated in a plane substantially at right angles to the optical axis of the microscope lens; - illumination beam scanning means allowing a displacement of the transverse illumination surface along the optical axis of the microscope lens; the microscopy system further comprising: - means for varying the focusing of the illumination beam, making it possible to laterally center the transverse illumination surface on the object imaging surface; - said means for varying the focusing being separate from the relative axial displacement means of the microscope lens and of the sample holder. - a sample holder; - a detection pathway comprising: - a microscope lens of given optical axis (Δ); - a detection device comprising a detection surface optically conjugate with an object imaging surface in the object space of the microscope lens; - means for relative axial displacement of the microscope lens and of the sample holder; - a microscope lens of given optical axis (Δ); - a detection device comprising a detection surface optically conjugate with an object imaging surface in the object space of the microscope lens; - means for relative axial displacement of the microscope lens and of the sample holder; - a sample illumination pathway comprising: - at least one emission source of an illumination beam; - means for forming, from the illumination beam, an illumination surface; - said microscope lens; - deflection means secured to the sample holder making it possible to deflect the illumination surface in the object space at the output of the microscope lens, to form a transverse illumination surface, situated in a plane substantially at right angles to the optical axis of the microscope lens; - illumination beam scanning means allowing a displacement of the transverse illumination surface along the optical axis of the microscope lens; - at least one emission source of an illumination beam; - means for forming, from the illumination beam, an illumination surface; - said microscope lens; - deflection means secured to the sample holder making it possible to deflect the illumination surface in the object space at the output of the microscope lens, to form a transverse illumination surface, situated in a plane substantially at right angles to the optical axis of the microscope lens; - illumination beam scanning means allowing a displacement of the transverse illumination surface along the optical axis of the microscope lens; - means for varying the focusing of the illumination beam, making it possible to laterally center the transverse illumination surface on the object imaging surface; - said means for varying the focusing being separate from the relative axial displacement means of the microscope lens and of the sample holder.