Quantifying methane (CH4) emissions from lakes is important for regional and global greenhouse gas emission inventories. However, regional and global estimates suffer from methodologically inconsistent data sets and from the situation that systematic flux measurements are presently available only for some regions in the world. In particular, many temperate regions dominated by agricultural land use, like central Europe, lack regional multi-lake studies of lacustrine CH4 emissions. We compare estimates of diffusive and ebullitive flux from 30 small central European and 17 small boreal lakes based on standardized measurements during a single visit per lake in late summer. Furthermore, we assess the amount of CH4 accumulated in the hypoxic deep-water layers in late summer. This provides an estimate of the potential release of CH4 from these lakes during autumn mixing (storage flux). The results show that emissions per unit area of lake surface from central European lakes are significantly higher than those from boreal lakes, with average estimates of diffusive and ebullitive flux being as much as six and 27 times higher, respectively. CH4 concentration in the surface water was significantly related with lake area and maximum depth in the boreal lakes. However, no significant relationships between diffusive and ebullitive fluxes and lake basin morphometry were found in central European or boreal lakes, as proposed in earlier studies, although the short measurement period (6 h) may not have been adequate for reliably quantifying ebullition in our study. As expected, storage flux was related to relative depth and relative volume of the hypoxic water layer in both regions. We discuss the relevance of the higher observed diffusive and ebullitive fluxes for regional estimates in central Europe based on an example of previous emission estimates from small lakes in Switzerland. Our results suggest that diffusive and ebullitive CH4 emissions from these lakes may be considerably higher than estimated based on widely applied relationships for predicting lacustrine CH4 emissions developed in northern European and North American regions. The results also confirm that modifications are necessary when applying these relationships to central European lakes. Our study highlights the inter-regional variability in lacustrine CH4 emissions and the need for regionally developed calibration data for validating and developing predictive models for estimating CH4 emissions from lakes at the landscape scale.