The objective of this work is to determine the prevalence of FI and associated factors in institutionalized elderly. A cross-sectional study is presented herein, conducted between October and December 2013, in 10 nursing homes (NHs) of the city of Natal (Northeast Brazil). Individuals over the age of 60 were included in the study, while those hospitalized or in terminal phase were excluded. Data collection included sociodemographic information, FI characterization, as well as variables related to the institution itself and to health conditions (comorbidities, medication, pelvic floor surgery, Barthel Index for functional capacity and Pfeiffer test for cognitive status). FI was verified through the Minimum Data Set (MDS) 3.0, which was also used to assess toileting programs. The Chi-square test and the linear Chi-square test were performed for bivariate analysis, as well as logistic regression for multivariate analysis. The final sample consisted of 321 elderly, mostly females, with mean age of 81.5 years. The prevalence of FI was 42.68% (CI 95%, 37.39-48.15). Most residents presenting FI were always incontinent (83.9%) and the most frequent incontinence type was total FI (solid and liquid stools). Incontinence control measures were applied only to 9.7% of the residents. The final model revealed a statistically significant association between FI and functional and cognitive impairments. It is concluded that FI is a health issue that affects almost half of the institutionalized elderly, and is associated with functional and cognitive disability.