The assignment of prognosis is one of the most important functions undertaken in clinical practice, yet there is little evidence to support the current decision-making process which is based on an outdated model of disease etiology and progression. This study evaluated 100 treated periodontal patients (2,484 teeth) under maintenance care for 5 years, with 38 of these patients followed for 8 years, to determine the relationship of assigned prognoses to the clinical criteria commonly used in the development of prognosis. The method of generalized estimating equations (GEE) for correlated data was utilized to determine the relationship of each clinical factor to the assignment of initial prognosis, improvement in prognosis at 5 years, and worsening in prognosis at 5 years. A multiple linear regression model was constructed for predicting initial prognosis based on initial clinical data. Increased probing depth, more severe furcation involvement, greater mobility, unsatisfactory crown-to-root ratio, malpositioned teeth, and teeth used as fixed abutments resulted in worse initial prognoses. The coefficients from this model were able to predict accurately the 5-year and 8-year prognoses 81% of the time. When teeth with "good" prognoses were excluded, the predictive accuracy dropped approximately 50%. Multiple logistic regression models indicated that improvement in prognoses and worsening in prognoses were both strongly associated with initial probing depth, initial furcation involvement, initial tooth malposition, and smoking when adjusted for initial prognosis. In addition, good hygiene was found to increase the probability of improvement in prognosis while initial mobility was found to decrease the likelihood of improvement in prognosis. Neither of these factors was found to be significant in worsening of prognosis. Smoking decreased the likelihood of improvement by 60% and doubled the likelihood of worsening in prognosis at 5 years. The results of this study indicate that some clinical factors used in the assignment of prognoses are clearly associated with changes in clinical condition over time. The data also demonstrated that the traditional approach for assigning prognoses is ineffective for teeth with an initial prognosis of less than good. Since most periodontally involved teeth are compromised, further work should include the development of a more effective method for assigning prognoses that is based on clear, objective clinical criteria.