Building-related symptoms in office workers worldwide are common, but of uncertain etiology. One cause may be contaminants related to characteristics of heating, ventilating, and air-conditioning (HVAC) systems. We analyzed data from 97 representative air-conditioned US office buildings in the Building Assessment and Survey Evaluation (BASE) study. Using logistic regression models with generalized estimating equations, we estimated odds ratios (OR) and 95% confidence intervals for associations between building-related symptom outcomes and HVAC characteristics. Outdoor air intakes less than 60 m above ground level were associated with significant increases in most symptoms: e.g. for upper respiratory symptoms, OR for intake heights 30 to 60 m, 0 to <30 m, and below ground level were 2.7, 2.0, and 2.1. Humidification systems with poor condition/maintenance were associated with significantly increased upper respiratory symptoms, eye symptoms, fatigue/difficulty concentrating, and skin symptoms, with OR = 1.5, 1.5, 1.7, and 1.6. Less frequent cleaning of cooling coils and drain pans was associated with significantly increased eye symptoms and headache, with OR = 1.7 and 1.6. Symptoms may be due to microbial exposures from poorly maintained ventilation systems and to greater levels of vehicular pollutants at air intakes nearer the ground level. Replication and explanation of these findings is needed. These findings support current beliefs that moisture-related HVAC components such as cooling coils and humidification systems, when poorly maintained, may be sources of contaminants that cause adverse health effects in occupants, even if we cannot yet identify or measure the causal exposures. While finding substantially elevated risks for poorly maintained humidification systems, relative to no humidification systems, the findings do not identify important (symptom) benefits from well-maintained humidification systems. Findings also provide an initial suggestion, needing corroboration, that outdoor air intakes lower than 18 stories in office buildings may be associated with substantial increases in many symptoms. If this is corroborated and linked to ground-level vehicle emissions, urban ventilation air intakes may need to be located as far above ground level as possible or to incorporate air cleaners that remove gaseous pollutants.