A 90-day rat inhalation study was performed in accordance with OECD test guideline 413 to characterize potential adverse effects caused by subchronic exposure to the Tobacco Heating System (THS) 2.2 aerosol, a heat-not-burn tobacco product, and to compare with those induced by the smoke generated from the reference cigarette 3R4F. Sprague Dawley rats were exposed for a period of 13 weeks to filtered air, three concentrations of mainstream 3R4F smoke (8, 15, 23 μg/l nicotine), or THS2.2 aerosol (15, 23, 50 μg/l nicotine). The evaluation of all OECD recommended endpoints indicated that aerosol from the THS2.2 caused a significantly reduced systemic and respiratory tract toxicity in comparison with cigarette smoke. The response of OECD endpoints may be only detectable after substantial damage. Therefore, the OECD endpoints were augmented with omics analysis generated from respiratory nasal epithelial (RNE) and lung tissue. Transcriptome analysis resulted in more than 3900 differential expressed genes (DEGs) in the RNE of male rats after 3R4F exposure, but in none after THS2.2 exposure. Gene set enrichment analysis using the KEGG database showed very few significant enrichment in THS2.2 groups. One gene set cluster was found that showed similar high enrichment as in the 3R4F groups. Processes belonged to amino acids, lipids and xenobiotics metabolism. Approximately 800 and 1300 DEGs were detected in lung tissue of male and female rats exposed to 3R4F, respectively. 17 DEGs were found in the lung tissue from THS2.2 exposed female rats. Ingenuity pathway analysis linked those genes to cellular movement and inflammatory responses. Overall, transcriptomics analysis showed a reduced response of THS2.2 on respiratory tissues compared with mainstream cigarette smoke.