Clouds exert an important influence on tropospheric photochemistry through modification of solar radiation that determines photolysis frequencies (J-values). We assess the radiative effect of clouds on photolysis frequencies and key oxidants in the troposphere with a global three-dimensional (3-D) chemical transport model (GEOS-CHEM) driven by assimilated meteorological observations from the Goddard Earth Observing System data assimilation system (GEOS DAS) at the NASA Global Modeling and Assimilation Office (GMAO). We focus on the year of 2001 with the GEOS-3 meteorological observations. Photolysis frequencies are calculated using the Fast-J radiative transfer algorithm. The GEOS-3 global cloud optical depth and cloud fraction are evaluated and generally consistent with the satellite retrieval products from the Moderate Resolution Imaging Spectroradiometer (MODIS) and the International Satellite Cloud Climatology Project (ISCCP). Results using the linear assumption, which assumes linear scaling of cloud optical depth with cloud fraction in a grid box, show global mean OH concentrations generally increase by less than 6% because of the radiative effect of clouds. The OH distribution shows much larger changes (with maximum decrease of ~20% near the surface), reflecting the opposite effects of enhanced (weakened) photochemistry above (below) clouds. The global mean photolysis frequencies for J[O1D] and J[NO2] in the troposphere change by less than 5% because of clouds; global mean O3 concentrations in the troposphere increase by less than 5%. This study shows tropical upper tropospheric O3 to be less sensitive to the radiative effect of clouds than previously reported (~5% versus 20~30%). These results emphasize that the dominant effect of clouds is to influence the vertical redistribution of the intensity of photochemical activity while global average effects remain modest, again contrasting with previous studies. Differing vertical distributions of clouds may explain part, but not the majority, of these discrepancies between models. Using an approximate random overlap or a maximum-random overlap scheme to take account of the effect of cloud overlap in the vertical reduces the impact of clouds on photochemistry but does not significantly change our results with respect to the modest global average effect.