The prevalence of chronic diseases has been rising in the recent years in developing countries. The long-term effects of the disease do not only cause huge financial burden on the country, but also likely have the huge impact on productivity. We examine the impact of several chronic diseases on the probability of labor participation using the data from the 2009 National Health Interview Survey in Taiwan. Using an endogenous multivariate probit model with recursive structures and instrumental variables, we control for the potential endogeneity of the incidence of chronic diseases such as heart disease, stroke and diabetes. The findings show that heart disease and stroke have negative effect on 18-39 year-old males and females. However, all diseases have negative effect on those in the 40-64 age groups.