Recent field observations in urban areas have shown that trace gases, such as O3, NO2, and NO3, develop distinct vertical concentration profiles at night. Because nocturnal chemistry can change the gas-phase and particulate composition in the urban boundary layer considerably, it is important to understand the mechanisms that lead to the change of trace gas levels with altitude. The quantification of the altitude dependence of chemical processes leading to the removal of volatile organic carbons (VOC) and NOx are crucial to assess the influence of nocturnal chemistry on ozone formation during the following day. We present a one-dimensional chemical transport model developed to study the interaction between chemistry and vertical transport in the nocturnal boundary layer. The model reproduces the general features found in field observations, such as positive O3 and NO3 gradients. The slow upward transport of NO and VOC emitted near the ground and the simultaneously occurring chemistry, in particular the reactions of NO with O3 and NO3, are found to control the vertical structure of the chemistry of NOx, NO3, N2O5, and VOC. In the case of NO2 and O3, dry deposition is also significant. The model results show that vertical transport of N2O5 plays an important role, and is often the main source of NO3 radicals near the ground. Chemical steady state calculations of the concentrations of NO3 and N2O5, as they have been used in the past, are therefore not representative in cases with significant vertical fluxes of N2O5. The vertical gradient of the oxidation rate of NO2 implies that the removal of NOx occurs predominately in the upper nocturnal boundary layer (NBL). Our study shows that observations at one altitude and chemical box models are often insufficient to accurately describe the chemistry in NBL.