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Malawi has a high maternal mortality rate, of which unsafe abortion is a major cause. About 140,000 induced abortions are estimated every year, despite there being a restrictive abortion law in place. This leads to complications, such as incomplete abortions, which need to be treated to avoid further harm. Although manual vacuum aspiration (MVA) is a safe and cheap method of evacuating the uterus, the most commonly used method in Malawi is curettage. Medical treatment is used sparingly in the country, and the Ministry of Health has been trying to increase the use of MVA. The aim of this study was to investigate the treatment of incomplete abortions in three public hospitals in Southern Malawi during a three-year period. All medical files from the female/gynecological wards from 2013 to 2015 were reviewed. In total, information on obstetric history, demographics, and treatment were collected from 7270 women who had been treated for incomplete abortions. The overall use of MVA at the three hospitals during the study period was 11.4% (95% CI, 10.7–12.1). However, there was a major increase in MVA application at one District Hospital. Why there was only one successful hospital in this study is unclear, but may be due to more training and dedicated leadership at this particular hospital. Either way, the use of MVA in the treatment of incomplete abortions continues to be low in Malawi, despite recommendations from the World Health Organization (WHO) and the Malawi Ministry of Health. © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).