In this paper, we present MESHAgents, a large-scale language model (LLM)-based multi-agent framework for cardiovascular disease imaging analysis. MESHAgents automatically identifies complex nonlinear dependencies between imaging phenotypes and disease risk factors and outcomes by leveraging multidisciplinary AI agents from cardiology, biomechanics, statistics, and clinical research. This is an attempt to overcome the limitations of existing human-centered hypothesis testing and correlated factor selection methods, and the performance of the system is validated through a population-based study using cardiac and aortic imaging phenotypes. MESHAgents identifies additional confounders beyond standard demographic factors, performs similarly to expert-selected phenotypes, and improves recall for specific disease types. It provides a scalable alternative to expert-driven approaches.