Aim: To investigate porous silicon (PSi) nanoparticles (NPs) behavior in the embryonic brain. Materials & methods: Fluorescently labeled PSi NPs were injected into the embryonic brains intraventricularly and to the mother intravenously (iv.). Brain histology from different time points up to 3 days was analyzed and live brains imaged with two-photon microscopy. Results: PSi NPs were able to penetrate 80% of the embryonic cortical depth. Particle motility was confirmed in real-time in vivo. PSi NPs were able to penetrate the embryonic cortex after either iv. maternal or intraventricular injection. No developmental of macromorphological changes or increased cell apoptosis was observed. Conclusion: PSi NPs penetrate deep in the brain tissues of embryos after intraventricular injection and after iv. injection to the mother.