This study aimed to verify health self-perception, its prevalence and associated factors in institutionalized elderly. A cross-sectional study is presented herein, conducted in 10 Long-Term care Institutions for the Elderly (LTIE) in the city of Natal (Northeast Brazil), between October and December 2013. Sociodemographic variables were analyzed, along with institution-related and health state variables. Descriptive and bivariate analyses were carried out (Chi-squared test, Fisher's exact test or linear trend Chi-squared test), as well as multivariate analysis (logistic regression). The final sample consisted of 127 elderly. The prevalence of negative self-perceived health was 63.19% (CI 95%: 55.07-70.63), and was associated with weight loss (PR: 1.54; CI 95%: 1.19-1.99), rheumatic disease (PR: 1.46; CI 95%: 1.05-2.01) and not-for-profit LTIE (PR: 1.37; CI 95%: 1.03-1.83), adjusted by sex. More than half of the elderly reported negative self-perceived health, which was associated with weight loss, rheumatic disease and type of institution. Actions must be developed to promote better health conditions in LTIE, such as nutrition consulting and physical therapy, to improve quality of life.