Lophomonas blattarum inhabits the intestines of cockroaches and mites. This study aimed to evaluate the existence of this protozoan parasite in bronchoalveolar lavage (BAL) samples of patients with respiratory disorders and nasal secretion samples of patients with sinusitis resistant to common treatments in Mashhad, Iran (between September 2014-October 2015). 133 samples were obtained from the patients, including 127 BAL samples (95.4%) and six nasal secretion samples (4.6%). Unexpected high rate of rarely known parasite “L blattarum” and its connection to upper respiratory infections and pneumonia cases were discovered. In total, 50 samples were positive for L. blattarum infection, 45 of which (33.8%) were BAL samples and five cases (3.7%) were nasal secretion samples. Since delayed diagnosis and treatment of pulmonary and sinus infection in our region due to L.blattarum contributes to higher mortality and morbidity, therefore, L.blattarum infection requires special attention as an emerging pathogen globally.