This article aims to investigate the morbidities related to medications, their risk factors and causes detected in patients who seek the Hospital Emergency Service of a University in the South of Brazil. Data collection was based on application of a questionnaire to patients of a minimum age of 18 years, that signing the Term of Free and Informed Consent (TFIC), during the period from October 2013 to March 2014, and analysis of electronic record charts. Cases were evaluated by pharmacists and a doctor to define whether it was a case of medication related morbidity (MRM) and to establish its possible causes. Avoidability of MRM was verified based on criteria previously established in the literature. In total 535 patients were interviewed, and the frequency of MRM was 14.6%, Approximately 45% of MRMs were related to safety in the use of medications, and approximately 50% presented user-related questions as the possible cause. Hospitalization was required in 44.8% of MRM cases; 62.7% of cases were considered avoidable. Presence of chronic disease and use of potentially dangerous medication and low therapeutic index were considered independent factors associated with development of MRM, according to statistical analysis.