Gastrointestinal problems such as diarrhoea have previously been reported in small studies among waste collectors. The present nationwide study relates self-reporteddiarrhoea symptoms to self-reported working conditions and estimated levels of bioaerosols. A questionnaire based survey among Danish waste collectors (n = 2303) and a comparison group of male municipality workers (n = 1430) collected data on occupational exposures, present and past working environment, psychosocial work environment, and health status. Estimated exposure was related to self-reported working conditions. Prevalence Proportion Ratios (PPR) adjusted for relevant confounders were estimated by generalized linear models. The group with high exposure to fungal spores reported most diarrhoea symptoms (PPR = 5.60 (2.39;13.08)), medium exposure was associated with fewer diarrhoea symptoms (PPR = 3.45 (2.24;5.31)), and the low exposure was associated with the fewest diarrhoea symptoms (PPR = 3.02 (1.86;4.92)). Test for trend was significant. The group with high exposure to either total count of fungi or total count of microorganisms reported fewest symptoms compared to the low exposed. No positive trend was found. This study reported an association between level of exposure to fungal spores and self-reported diarrhoea among waste collectors