Succinic semialdehyde dehydrogenase deficiency (SSADHD) represents a rare monogenetic, autosomal-recessive disorder causing an enzymatic block of the degradation of gamma-aminobutyric acid (GABA) due to variants in ALDH5A1. Succinic semialdehyde cannot be converted to succinate and is consecutively converted to gamma-hydroxybutyrate (GHB). The phenotype is comprised of developmental delay, motor difficulties, behavioral problems and epilepsy. It is unclear how altered concentrations of GABA and GHB contribute to the pathophysiology of SSADHD. We used patient-derived iPSCs to generate a three-dimensional cerebral organoid model to study early neuronal development in SSADHD organoids. Immunohistochemistry and whole-cell patch clamp were used to determine morphological and electrophysiological properties. Early stage SSADHD organoids revealed structural alterations revealing decreased ventricular thickness and decreased area size of the ventricle-like structures compared to control organoids. Further analysis revealed premature neuronal differentiation with an overall reduction of neuronal progenitor cells. Moreover, mitotic activity of resident progenitor cells seems to be significantly decreased in SSADHD organoids compared to control organoids. These findings point towards structural differences strongly influenced by premature neuronal differentiation and a decreased pool of stem cells or early cell cycle exit. Nevertheless, neurons of SSADHD organoids are functionally active revealing neuron-typical electrophysiological properties such as resting membrane potential and repetitive action potentials upon stimulation. We propose an unprecedented role of GABA and GHB as a cause for alterations of SSADHD organoids modelled in patient-derived three-dimensional organoid system. This novel technique can be used to study fine structural differences of disease and control organoids as mentioned above.