In this thesis uncertainty associated with stock assessment has been considered, especially uncertainty associated with the input data to the model. The thesis provides new approaches to analyse the sources of variation in the input data and their magnitude, and an alternative approach for modelling the dynamics of a fish population is suggested. A new approach is introduced to analyse the sources of variation in age composition data, which is one of the most important sources of information in the cohort based models for estimation of stock abundancies and mortalities. The approach combines the continuation-ratio logits, which can take the ordinal and multinomial characteristics of the response into account, and the generalized linear mixed models, which allow for fixed as well as random effects to be analysed. Catch at age data and the associated uncertainties have been estimated, by separating the statistical analysis into separate analyses of the various data sources. The results were combined into estimates of the catch at age data and the associated uncertainties for the sandeel landings from the North Sea in 1989 and 1991. An overview of age-structured stock assessment models is given and it is argued that an approach utilising stochastic differential equations might be advantagous in fish stoch assessments.