This study aimed to characterise the relationship between adverse health outcomes and occupational risk factors among workers at a soy processing plant. A questionnaire, spirometry, methacholine challenge, immune testing and air sampling for dust and soy were offered. Prevalence ratios (PRs) of respiratory problems from comparisons with the US adult population were calculated. Soy-specific immunoglobulin (Ig)G and IgE among participants and healthcare worker controls were compared. Associations between health outcomes and potential explanatory variables were examined using logistic regression. 147 (52%) out of 281 employees, including 66 (70%) out of 94 production workers, participated. PRs were significantly elevated for wheeze, sinusitis, ever-asthma and current asthma. Participants had significantly higher mean concentrations of soy-specific IgG (97.9 mg·L(-1) versus 1.5 mg·L(-1)) and prevalence of soy-specific IgE (21% versus 4%) than controls. Participants with soy-specific IgE had three-fold greater odds of current asthma or asthma-like symptoms, and six-fold greater odds of work-related asthma-like symptoms; the latter additionally was associated with production work and higher peak dust exposures. Airways obstruction was associated with higher peak dust. Work-related sinusitis, nasal allergies and rash were associated with reported workplace mould exposure. Asthma and symptoms of asthma, but not other respiratory problems, were associated with immune reactivity to soy.