Methane is an important atmospheric chemical compound and greenhouse gas. It plays a major role in the chemistry of tropospheric ozone, OH, and CO, especially in remote areas. Newly available measurements of methane from space provide the potential to revolutionize our understanding of this trace gas. However, there are significant issues regarding the effects of clouds and aerosols on the retrievals that impact the comparison of these retrievals with 3D chemical transport models. In this study, we compared our 3D model (MATCH driven by NCEP reanalysis data) simulations of methane column burdens with remotely sensed data from SCIAMACHY for the year 2003. Model simulations agree well with observations in terms of their spatial distribution, but they have a 2.7 x 1018 molecules/cm2 offset (or ~ 8 % of the total CH4 column) compared with observations. In order to understand and resolve this offset, we further investigated the impact of cloud and aerosols on methane column estimates. The correlation of SCIAMACHY methane column with observed cloud top height, estimated using the FRESCO scheme, increases with the cloud fraction. When the sky is overcast, they are linearly correlated with an r2 of ~ 0.8. After the FRESCO cloud information, including cloud fraction and effective cloud height, is incorporated, we found that the model- satellite comparison splits into two branches: one is correlated with the cloud top height, while the other is not, especially when the cloud fraction is small. We then tested the potential impact of aerosols on the methane column retrievals. Direct comparison of SCIAMACHY methane column burden with MODIS AOD shows complicated relations since aerosols can attenuate retrievals of the methane column on one hand, while the sources of aerosols and methane could be collocated on the other. We further compared the aerosol characteristics for the two branches which the model-observation methane column burden comparison had split into to help resolve the above offset.