Abstract COVID-19 typically causes respiratory disorders, but several COVID-19 patients (30–60%) manifest also a wide range of neurological conditions, advocating for detrimental effects of SARS-CoV-2 or Spike (S) protein on the central nervous system. However, the molecular mechanisms responsible for these disfunctions as well as the potential neurotropism of SARS-CoV-2, are still under investigation. To assess this issue, by using iPSC-derived-human brain organoids (HBO) we evaluated: the expression of SARS-CoV-2 main receptors: ACE2, CD147, NRP1, Furin, TMPRSS2 (qPCR, IF); their infectability by SARS-CoV-2 over-time (QPCR, TCID50, IF); and the effect of SARS-CoV-2-infection and S exposure on HBO transcriptome (qPCR) and secretome (Multiplex ELISA). All the main SARS-CoV-2 receptors are expressed by HBO with lower NRP1 levels compared to CD147 and ACE2. By analyzing viral N1and N2gene sequence over time, infectability of VeroE6 cells by SARS-CoV-2 infected HBO supernatants, and nucleocapsid expression by IF we confirmed that HBO may be productively infected by the virus. Furthermore, SARS-CoV-2 infection was accompanied by the activation of apoptotic and stress pathways (caspase3, caspase8, Bcl2, S100B), inflammatory process (CCL2, NLRP3) Interferon Stimulated Genes (IFITM1, IFITM3, STAT1, NFkB) and antigen presentation pathway (ERAP1, ERAP2, HLA-A, TAP). Notably, the trend of the different targets was comparable following SARS-CoV-2 infection and S-stimulation. These results confirm that SARS-CoV-2 infect HBO probably by binding CD147 and ACE2 receptors and indicate that the exposure to the S protein can affect their homeostasis and exert neurotoxic effects presumably driving the so called long-COVID symptoms. Partially supported by grants from Fondazione Alessandro and Vincenzo Negroni Prati Morosini and Fondazione Romeo and Erica Invernizzi.