We discuss estimation and prediction in a Markov renewal model where intensities of the one-step transitions follow a Cox regression model with baseline hazards and covariates depending on the backward recurrence time. A modification of the Andersen and Gill results is given to extend the asymptotic properties of the partial likelihood estimates to this setting. We further consider prediction of the realization of the process in a single individual based on the follow-up information. Data of the International Bone Marrow Transplant Registry are used for illustration purposes.