Uncertainty research represents a research stream of high interest within the community of geographical information science. Its elements, terminology and typology are still under strong discussion and adopted methods for analysis are currently under intensive development. This paper presents a conceptual framework for systematic investigation of uncertainty which occurs in applications of land cover change modelling in Geographical Information Systems (GIS) based on historical map data. Historical, in this context, means the map is old enough to allow identification of changes in landscape elements of interest, such as vegetation. To date such analyses are rarely conducted or not satisfactorily carried out, despite the fact that historical map data represent a potentially rich information source. The general validity and practicability of the framework for related applications is demonstrated with reference to one example in which forest cover change in Switzerland is investigated. The conceptual model consists of three domains in which main potential sources of uncertainty are systematically exposed. Existing links between data quality research and uncertainty are investigated to access the complex nature of uncertainty and to characterise the most suitable concepts for analysis. In accordance with these concepts appropriate methods and procedures are suggested to assess uncertainty in each domain. One domain is the production‐oriented amount of uncertainty which is inherent in the historical map. Vagueness and ambiguity represent suitable concepts for analysis. Transformation‐oriented uncertainty as the second domain occurs owing to editing and processing of digital data. Thereby, the suitable concept of uncertainty is error. The third domain is the application‐oriented uncertainty which occurs in comparing semantically different data. This domain relates to multi‐temporal discord which assumes the assessment of ‘equi‐temporal’ ambiguity and is thus connected to the production‐oriented domain. The framework provides an estimation of the overall amount of uncertainty. This can be linked to subsequent assessment of ‘fitness for use’. Thus the model provides a practicable and systematic approach to access the complex nature of uncertainty in the scope of land cover change modelling.