The model introduced for the natural history of a progressive disease has four disease states which are expressed as a joint distribution of three survival random variables. Covariates are included in the model using Cox’s proportional hazards model with necessary assumptions needed. Effects of the covariates are estimated and tested. Formulas for incidence in the preclinical, clinical and death states are obtained, and prevalence formulas are obtained for the preclinical and clinical states. Estimates of the sojourn times in the preclinical and clinical states are obtained.