Background: Available evidence shows that tetracycline family has cellular and molecular mechanisms to protect neurons and oligodendrocytes by modulating matrix metalloproteinases. We tried to compare the effectiveness of intramuscular and subcutaneous interferon beta-1a (INF-β1a) in combination with oral doxycycline among patient with relapsing remitting multiple sclerosis (RRMS) and secondary progressive multiple sclerosis (SPMS).Methods: A double-blind clinical trial study was conducted at Hamedan University of Medical and Health Sciences in Iran. Sixty patients with definite diagnosis of RRMS or SPMS were treated with doxycycline and 44 µg subcutaneous IFN-β1a three times a week or 30 µg intramuscular IFN-β1a once a week for six months. Neurologic examinations were performed monthly until the end of the treatment. Changes in expanded disability status scale (EDSS) scores, brain magnetic resonance images (MRIs), and frequency of receiving corticosteroid pulse were evaluated before and after the treatment.Results: Women constituted 88.3% of the participants. The mean age of the patients was 32 years. The mean EDSS scores reduced from 4.5 to 3.0. Based on the frequency of receiving corticosteroid pulse, relapse rate decreased from 3.2 to 0.8. MRI showed that the number, volume, and activity of the lesions decreased among 13.3% of the participants, increased among 15%, and remained persistent among 71.7%.Conclusion: Combination of doxycycline and IFN-β1a can decrease relapse rate and improve EDSS scores in patients with RRMS and SPMS. However, it does not affect MRI changes. Furthercontrolled clinical trials on greater number of patients with MS are needed to evaluate the efficacy of combination therapy.