Background Classification of the periodontal conditions is indispensable for epidemiological data in order to guide situational awareness and therapeutic strategies. The new classification of periodontal diseases and conditions introduced by the American Academy of Periodontology and the European Federation of Periodontology (AAP/EFP), however, has not yet been applied to population-based studies. The aim of the present study was to compare the prevalence of periodontitis between the AAP/EFP and the CDC/AAP classification system and to evaluate the accuracy of the new AAP/EFP classification system against the CDC/AAP case definition for population-based studies. Methods Epidemiological data from two cross-sectional studies were obtained. One of them was a population-based study on Chilean adults (1.456 individuals; 35-44 years; 65-74 years) and the other one a sample of adolescents (1.070 individuals; 15-19 years) from five countries; Argentina, Chile, Colombia, Ecuador, and Uruguay. All participants had undergone full-mouth periodontal examination by calibrated examiners. Epidemiological datasets were analyzed according to the AAP/EFP and the CDC/AAP case definitions. The accuracy of the AAP/EFP definition was examined by assessing the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the receiver operating curve (ROC) using the CDC/AAP case definition as the reference standard. Results According to the AAP/EFP, the prevalence of periodontitis in adolescents was 75.6%. The majority of the adolescents were classified either as Stage I (39.2%) or Stage II (28.2%). By using the CDC/AAP classification the prevalence of periodontitis in adolescents was 27.2%. The most common form of periodontitis with the CDC/AAP classification was moderate periodontitis (15.3%) followed by mild periodontitis (11.4%). The AAP/EFP revealed high sensitivity in moderate (95.7%) and severe periodontitis (100%) as well as a moderate (75%) to high specificity (92%) in moderate and severe periodontitis, respectively. The PPV was 41.6% in moderate and 5.7% in severe periodontitis whereas the NPV was high in both categories (moderate = 99%; severe = 100%). The AUC was 0.91 (95% CI = 0.89-0.93). In adults, the prevalence of periodontitis was 99% according to the AAP/EFP. The majority of adults were classified as Stage IV (81.3%) whereas Stage III amounted to 12.8%. By using the CDC/AAP classification, the prevalence of periodontitis in adults was 88.3% and the most common form of periodontitis was moderate periodontitis (57.2%) followed by severe periodontitis (29.7%). In adults, the AAP/EFP revealed high sensitivity for moderate (99.7%) and severe periodontitis (100%), but low specificity for both categories (moderate = 6.8%; severe = 8.3%). The PPV was 88.7% in moderate and 31.7% in severe periodontitis. The NPV was high in both categories (moderate = 76.5%; severe = 100%). The AUC was 0.57 (95% CI = 0.53-0.62). Conclusions This study revealed a clear discrepancy in the prevalence of periodontitis between the AAP/EFP and the CDC/AAP classification when using epidemiological data. The 2017 AAP/EFP classification system performs well when compared to the CDC/AAP case definition in identifying adolescents with periodontitis. The AAP/EFP system seems less accurate in adults with high prevalence of periodontitis.