Diffusion models have demonstrated appealing performance in both image and video generation. However, many works discover that they struggle to capture important, high-level relationships that are present in the real world. For example, they fail to learn physical laws from data, and even fail to understand that the objects in the world exist in a stable fashion. This is due to the fact that important conditional dependence structures are not adequately captured in the vanilla diffusion models. In this work, we initiate an in-depth study on strengthening the diffusion model to capture the conditional dependence structures in the data. In particular, we examine the efficacy of the auto-regressive (AR) diffusion models for such purpose and develop the first theoretical results on the sampling error of AR diffusion models under (possibly) the mildest data assumption. Our theoretical findings indicate that, compared with typical diffusion models, the AR variant produces samples with a reduced gap in approximating the data conditional distribution. On the other hand, the overall inference time of the AR-diffusion models is only moderately larger than that for the vanilla diffusion models, making them still practical for large scale applications. We also provide empirical results showing that when there is clear conditional dependence structure in the data, the AR diffusion models captures such structure, whereas vanilla DDPM fails to do so. On the other hand, when there is no obvious conditional dependence across patches of the data, AR diffusion does not outperform DDPM.