To determine in patients admitted with an acute exacerbation of chronic obstructive pulmonary disease (AE-COPD) the association between the isolation of potential pathogens in a conventional sputum culture and comorbidities. The ESMI study is a multicenter observational study. Patients with AE-COPD admitted to the Internal Medicine departments of 70 hospitals were included. The clinical characteristics, treatments, and comorbidities were gathered. The results of conventional sputum cultures were recorded. A total of 536 patients were included, of which 161 produced valid sputum and a potentially pathogenic microorganism was isolated from 88 subjects (16.4%). The isolation of Pseudomonas aeruginosa (30.7%) was associated with a greater severity of the lung disease (previous admissions [ P = 0.026], dyspnea scale [ P =0.047], post-broncodilator forced expiratory volume in 1 second (FEV) [ P =0.005], and the BODEx index [ P =0.009]); also with higher prevalence of cor pulmonale (P =0.017), heart failure (P =0.048), and cerebrovascular disease (P =0.026). Streptococcus pneumoniae (26.1%) was associated with more comorbidity according to number of diseases (P =0.018); notably, peripheral artery disease (P =0.033), hypertension (P =0.029), dyslipidemia (P =0.039), osteoporosis (P =0.0001), and depression (P =0.005). Patients with AE-COPD and P. aeruginosa present higher severity of COPD, while those with S. pneumoniae present greater comorbidity. The potentially pathogenic microorganism obtained in the sputum culture depends on the associated comorbidities.