Agriculture has been implicated as a potential driver of human infectious diseases. However, the generality of disease-agriculture relationships has not been systematically assessed, hindering efforts to incorporate human health considerations into land-use and development policies. Here we perform a meta-analysis with 34 eligible studies and show that people who live or work in agricultural land in Southeast Asia are on average 1.74 (CI 1.47-2.07) times as likely to be infected with a pathogen than those unexposed. Effect sizes are greatest for exposure to oil palm, rubber, and non-poultry based livestock farming and for hookworm (OR 2.42, CI 1.56-3.75), malaria (OR 2.00, CI 1.46-2.73), scrub typhus (OR 2.37, CI 1.41-3.96) and spotted fever group diseases (OR 3.91, CI 2.61-5.85). In contrast, no change in infection risk is detected for faecal-oral route diseases. Although responses vary by land-use and disease types, results suggest that agricultural land-uses exacerbate many infectious diseases in Southeast Asia.