Many process-based models of carbon (C) and nitrogen (N) cycles have been developed for northern forest ecosystems. These models are widely used to evaluate the long-term decisions in forest management dealing with effects like particulate pollution, productivity and climate change. Regarding climate change, one of the key questions that have sensitive political implications is whether northern forests will sequester atmospheric C or not. Whilst many process-based models have been tested for accuracy by evaluating or validating against observed data, few have dealt with the complexity of the incorporated procedures to estimate uncertainties associated with model predictions or the sensitivity of these predictions to input factors in a systematic, inter-model comparison fashion. In general, models differ in their underlying attempts to match natural complexities with assumed or imposed model structure and process formulations to estimate model parameters, to gather data and to address issues on scope, scale and natural variations. Uncertainties may originate from model structure, estimation of model parameters, data input, representation of natural variation and scaling exercises. Model structure relates to the mathematical representation of the processes modelled and the type of state variables that a model contains. The modelling of partitioning among above- and below-ground C and N pools and the interdependence among these pools remain a major source of uncertainty in model structure and error propagation. For example, most soil C models use at least three state variables to represent the different types of soil organic matter (SOM). This approach results in creating three artificial SOM pools, assuming that each one contains C compounds with the same turnover rate. In reality, SOM consists of many different types of C compounds with widely different turnover rates. Uncertainty in data and parameter estimates are closely linked. Data uncertainties are associated with high variations in estimating forest biomass, productivity and soil organic matter and their estimates may be incomplete for model initialisation, calibration, validation and sensitivity analysis of generalised predictor models. The scale at which a model is being used also affects the level of uncertainty, as the errors in the prediction of the C and N dynamics differ from site to landscape levels and across climatic regions. If the spatial or temporal scale of a model application is changed, additional uncertainty arises from neglecting natural variability in system variables in time and space. Uncertainty issues are also intimately related to model validation and sensitivity analysis. The estimation of uncertainties is needed to inform decision processes in order to detect the possible corridor of development. Uncertainty in this context is an essential measure of quality for stakeholder and decision makers.