Nocturnal chemistry in urban areas can considerably influence the composition of the boundary layer by removing nitrogen oxides and hydrocarbons, as well as changing the size and composition of aerosol particles. Although these processes can have a severe impact on pollution levels at night and during the following day, little quantitative information is available. In particular, the vertical variation of trace gas concentrations and chemistry at night has received little attention and is thus poorly understood. Here we present differential optical absorption spectroscopy (DOAS) measurements of the vertical distributions of O3, NO2, and NO3 during the Texas Air Quality Study 2000 near Houston, TX. Distinct vertical profiles, with lower mixing ratios of O3 and NO3 near the ground than above 100 m altitude, were observed. Mixing ratios of NO3 aloft reached 50 ppt and above, and steady state N2O5 levels were calculated to be 100--300 ppt. A one-dimensional chemical transport model reveals that the formation of the vertical trace gas distributions is driven by deposition, surface emissions of NO, reactions of O3 and NO3, and vertical mixing. The removal of O3 in Houston is found to proceed by dry deposition, while NOx is primarily lost above 10 m altitude by N2O5 chemistry. The study shows that chemistry in polluted areas is strongly altitude dependent in the lowest 100 m of the nocturnal atmosphere. This altitude dependence should be considered in future field and model studies of urban air pollution.