We investigate long-term productivity trends in a representative intensive rice cropping system using periodic farm level survey data spanning more than 20 years of the Green Revolution in two rice bowls of the Philippines. Estimation of production functions with year dummy variables shows substantial declines in productivity from the early 1980s to the mid-1990s. Examination of secondary data shows, however, that the survey years were unrepresentative of long-term trends and were unduly influenced by exogenous yield shocks. Correction for these effects removes the productivity decline, but shows that productivity has stagnated. A renewed emphasis on increasing crop genetic yield potential may be necessary in order to improve productivity and restore the contribution of this important farming system to poverty alleviation.