Recently, we have reported that primary particles from diesel exhaust affect nervous system, immune system, and learning ability in mice. Currently, in vivo and in vitro studies have shown that secondary organic aerosol (SOA) generated from the coal-fired power plant induced adverse effects in lung and heart. However, the effect of SOA on central nervous system is still unknown. In the present study, using potential biomarkers recognized in previous studies of primary particles, we investigated the effect of acute single administration of SOA on the expression levels of various biomarkers in the brain and lung of mice. We generated the SOA by addition of ozone (O₃) to the diesel exhaust particle (DEP). Eight-week-old male BALB/c mice were administered DEP or DEP+O₃ (SOA) (50 µg/50 µl/mouse) intranasally. Twenty-four hour after acute single exposure to SOA, olfactory bulb, hippocampus and lung from all mice were collected and mRNA expressions of neurological and immunological biomarkers were examined using real-time RT-PCR analysis and histological examination. Proinflammatory cytokines, their transcription factor and neurotrophin mRNA were remarkably increased in lung of mice exposed to SOA but not in the brain. Microarray data showed that changes of the inflammatory reaction and metabolizing enzyme gene cluster were observed in the brain and lung. Our findings suggested that an acute single exposure of SOA does not affect biomarkers in the brain of normal healthy individuals. Our present results also clearly indicate that SOA induces inflammatory responses in the lung by modulating proinflammatory cytokines, transcription factor and inflammatory responsive neurotrophins.