Waterpipe smoking is one of the most popular methods of tobacco consumption worldwide which induces many health problems. In the present study; we evaluated the toxic effects of waterpipe smoke by using amiodarone as a model for lung toxicity in adult male albino rats. Also, the protective and therapeutic effects of carob aqueous extract on these toxicity which produced by daily exposure to waterpipe smoke for 8 weeks. The amiodarone gavage significantly increased serotonin content in brainstem and cerebral cortex after 8 and 2 weeks respectively and dopamine content at most of time intervals. Moreover, waterpipe smoke exposure induced a significant decrease in dopamine content after 2 weeks in brainstem and in serotonin content after 4, 6 weeks in brainstem and 6, 8 weeks in cerebral cortex. While, increment in dopamine content after 4, 6 weeks in brainstem and 6, 8 weeks in cerebral cortex may be due to increase its synthesis which strengthens the coughing reflex. Amiodarone gavage and waterpipe smoke exposure induced a significant increase in myeloperoxidase activity, hydroxyproline content and nitric oxide level in lung; while, catalase activity was decreased significantly. Consequently, waterpipe smoke exposure for long time caused serious harmful effects on brain and lung nearly like amiodarone. Carob extract pre-and post-treatment has the ability to protect and ameliorate these effects due to its antioxidant and anti-coughing effects. So, further studies are necessary to elucidate the mechanism of action of the effective components in the extract.