Few studies have measured the effect of short-term exposure to industrial emissions on the respiratory health of children. Here we estimate the risk of hospitalization for asthma and bronchiolitis in young children associated with their recent exposure to emissions from an aluminum smelter. We used a case-crossover design to assess the risk of hospitalization, February 1999-December 2008, in relation to short-term variation in levels of exposure among children 0-4 years old living less than 7.5 km from the smelter. The percentage of hours per day that the residence of a hospitalized child was in the shadow of winds crossing the smelter was used to estimate the effect of wind-borne emissions on case and crossover days. Community-wide pollutant exposure was estimated through daily mean and daily maximum SO2 and PM2.5 concentrations measured at a fixed monitoring site near the smelter. Odds ratios (OR) were estimated using conditional logistic regressions. The risk of same-day hospitalization for asthma or bronchiolitis increased with the percentage of hours in a day that a child’s residence was downwind of the smelter. For children aged 2-4 years, the OR was 1.27 (95% CI = 1.03-1.56; n = 103 hospitalizations), for an interquartile range (IQR) of 21% of hours being downwind. In this age group, the OR with PM2.5 daily mean levels was slightly smaller than with the hours downwind (OR: 1.22 for an IQR of 15.7 μg/m3, 95% CI = 1.03-1.44; n = 94 hospitalizations). Trends were observed between hospitalizations and levels of SO2 for children 2-4 years old. Increasing short-term exposure to emissions from a Quebec aluminum smelter was associated with an increased risk of hospitalization for asthma and bronchiolitis in young children who live nearby. Estimating exposure through records of wind direction allows for the integration of exposure to all pollutants carried from the smelter stack.