Objective: To explore associations between mean discrepancy values for the first and second molars (MDVFSs) and generalised aggressive periodontitis (GAgP) using hospital-based periodontal examination records from a large Chinese population. Methods: Data from consecutive patients diagnosed as having chronic periodontitis (CP, n = 51,849) and GAgP (n = 2,706) were included. Patient ages, gender, smoking status, mean full-mouth probing depth (PD), and mean full-mouth attachment loss (AL), as well as MDVFSs for PD and AL, were extracted. Multivariate linear regression was used to test associations between MDVFSs and GAgP. Results: After multivariate risk adjustment for potential confounding factors (age, smoking status, and mean PD and AL), the MDVFSs for PD (OR = 2.20, 95%CI: 2.04 to 2.38, P 0.001) and AL (OR = 1.51, 95CI%: 1.44 to 1.59, P 0.001) were significantly associated with GAgP. The probability of GAgP was associated with MDVFS for PD falling between 0 mm and 2.5 mm (OR = 4.55, 95%CI: 4.01 to 5.17) and MDVFS for AL falling between 0 mm and 3.5 mm (OR = 2.01, 95%CI: 1.86 to 2.16, P 0.001). Conclusion: This study revealed associations between MDVFSs and GAgP, demonstrating that MDVFSs can serve as promising auxiliary references for the differential diagnosis between CP and GAgP. Keywords: aggressive periodontitis, chronic periodontitis, diagnosis