The generalized estimation equation (GEE) method, one of the generalized linear models for longitudinal data, has been used widely in medical research. However, the related sensitivity analysis problem has not been explored intensively. One of the possible reasons for this was due to the correlated structure within the same subject. We showed that the conventional residuals plots for model diagnosis in longitudinal data could mislead a researcher into trusting the fitted model. A non-parametric method, named the Wald–Wolfowitz run test, was proposed to check the residuals plots both quantitatively and graphically. The rationale proposedin this paper is well illustrated with two real clinical studies in Taiwan. Copyright © 2000 John Wiley & Sons, Ltd.