Indoor air quality has become increasingly important as we live in a society where the majority of our time is spent indoors. Specific attention has been drawn to airborne fungal spores as a factor affecting indoor air quality. This study targeted shortcomings of other studies by utilizing long‐term air sampling and total fungal spore enumeration to determine associations between health outcomes and fungal spore concentrations. Infants (n=144) were clinically evaluated and had skin prick tests (SPT) for 17 allergens. Airborne fungal spores were collected using a Button Personal Inhalable Sampler (SKC Inc.) for 48h at a flow rate of 4l/min. Sampling was conducted in the spring (March–May) or fall (August–October) in 2003–2004. Fungal spores were analyzed using microscopy‐based total counting and identified to the genus/group level. Total spore and individual genus concentrations were analyzed for associations with rhinitis and positive SPT results. Overall, concentrations varied widely, between <2 and 2294 spores/m3. While no relationship was observed between SPT(+) and total fungal counts, several significant associations were found when analysis was conducted on the various fungal genera and health outcomes. Positive associations were obtained between: Basidiospores and rhinitis (p<0.01), Penicillium/Aspergillus and SPT(+) to any allergen (p<0.01), and Alternaria and SPT(+) to any allergen (p<0.01). Inverse associations were found between: Cladosporium and SPT(+) to any allergen (p<0.05), and Cladosporium and SPT(+) to aeroallergens (p<0.05). This study indicates that health outcome may vary by fungal genera; some fungal types may have sensitizing effects while others may have a beneficial role.