BACKGROUND: We have previously found regional differences in the prevalence of known type 2 diabetes between northeastern and southern Germany. We aim to also provide prevalence estimates for prediabetes (isolated impaired fasting glucose (i-IFG), isolated glucose intolerance (i-IGT), combined IFG and IGT) and unknown type 2 diabetes for both regions. METHODS: Prevalence (95%CI) of prediabetes (i-IFG: fasting glucose 5.6-6.9 mmol/l; i-IGT: 2 h postchallenge gluose 7.8-11.0 mmol/l, oral glucose tolerance test (OGTT), ≥8 h overnight fasting) and unknown diabetes were analyzed in two regional population-based surveys (age group 35-79 years): SHIP-TREND (Study of Health in Pomerania (northeast), 2008-2012) and KORA F4 (Cooperative Health Research in the region of Augsburg (south), 2006-2008). Both studies used similar methods, questionnaires, and identical protocols for OGTT. Overall, 1,980 participants from SHIP-TREND and 2,617 participants from KORA F4 were included. RESULTS: Age-sex-standardized prevalence estimates (95%CI) of prediabetes and unknown diabetes were considerably higher in the northeast (SHIP-TREND: 43.1%; 40.9-45.3% and 7.1%; 5.9-8.2%) than in the south of Germany (KORA F4: 30.1%; 28.4-31.7% and 3.9%; 3.2-4.6%), respectively. In particular, i-IFG (26.4%; 24.5-28.3% vs. 17.2%; 15.7-18.6%) and IFG+IGT (11.2%; 9.8-12.6% vs. 6.6%; 5.7-7.5%) were more frequent in SHIP-TREND than in KORA. In comparison to normal glucose tolerance, the odds of having unknown diabetes (OR, 95%CI: 2.59; 1.84-3.65) or prediabetes (1.98; 1.70-2.31) was higher in the northeast than in the south after adjustment for known risk factors (obesity, lifestyle). CONCLUSIONS: The regional differences of prediabetes and unknown diabetes are in line with the geographical pattern of known diabetes in Germany. The higher prevalences in the northeast were not explained by traditional risk factors.