To estimate disability-adjusted life years (DALY) and cost of illness (COI) associated with the gastrointestinal bacterial pathogens Campylobacter and verocytotoxin-producing Escherichia coli (VTEC) in Sweden and to investigate the impact of variability in health outcomes, data availability, and different assumptions about underreporting on DALY. Data from the Swedish notification system, public databases, and the literature were used to estimate COI and DALY. DALY was modelled using a deterministic and a stochastic approach, the latter describing variation in health outcomes between individuals. Effects of different assumptions about underreporting of gastroenteritis were evaluated in separate scenarios. COI and DALY were greater for Campylobacter than for VTEC. Years of life lost due to haemolytic uraemic syndrome and years lived with gastroenteritis constituted most of DALY for VTEC and Campylobacter, respectively. Productivity losses due to gastroenteritis constituted the main cost associated with both pathogens. Degree of underreporting had a greater impact on DALY for Campylobacter, due to higher estimated incidence of gastroenteritis associated with campylobacteriosis. Pathogen-specific health outcomes and data quality may influence the preferred modelling approach. There was a fair agreement between modelling approaches, but the stochastic model reflected the contribution of some rare health outcomes not captured in the deterministic model. Health outcomes excluded due to lack of data lead to an underestimation of the total burden associated with the pathogens. Increased knowledge, especially on the degree of underreporting and the contribution of the pathogens to sequelae, is needed to further improve public health burden estimates for these pathogens in Sweden.