This paper studies estimation in panel vector autoregression (VAR) under cross-sectional dependence. The time series are allowed to be an unknown mixture of stationary and unit root processes with possible cointegrating relations. The cross-sectional dependence is modeled with a factor structure. We extend the factor analysis in Bai and Ng (2002, Econometrica 70, 191–221) to vector processes. The fully modified (FM) estimator in Phillips (1995) is used for estimation in panel VAR and we also propose a factor augmented FM estimator. Our simulation results show this factor augmented FM estimator performs well when sample size is large.