Background This retrospective study evaluated and assigned scores to six prognostic factors and derived a quantitative scoring system used to determine the periodontal prognosis on molar teeth. Methods Data were gathered on 816 molars in 102 patients with moderate to severe periodontitis. The six factors evaluated, age, probing depth, mobility, furcation involvement, smoking, and molar type, were assigned a numerical score based on statistical analysis. The sum of the scores for all factors was used to determine the prognosis score for each molar. Only patients with all first and second molars at the initial examination qualified for the study. All patients were a minimum of 15 years post treatment. Results The post treatment time ranged from 15 to 40 years and averaged 24 years. When the study was completed, 639 molars survived (78%), and of those surviving molars, 566 survived in health (89%). In molars with lower scores (1,2,and 3) the 15-year survival rates ranged from 99% to 96%. For scores 4, 5, 6 the 15 year survival rates ranged was 95% to 90% and for molars with scores of 7, 8, 9, and 10 the survival rates ranged from 86% to 67%. Conclusions Our results indicate that the periodontal prognosis on molars diagnosed with moderate to severe periodontitis can be calculated using an evidence-based scoring system.