To date no study in Benin has attempted to determine whether there has been productivity growth in the hospital sector as a result of the various health sector reforms undertaken in the recent past.The objective of this study was to assess the changes in productivity of zone hospitals in Benin over five years (2003-2007) with a view to analysing source of the change.Methods:Malmquist data envelopment analysis method was used to analyze productivity among a sample of 23 zonal public hospitals in the Republic of Benin over a period of five years, i.e. 2003 to 2007. Health inputs and utilization data was collected from records of sampled hospitals through physical visits by one of the authors. Results: Ten (43.5 per cent) out of 23 hospitals experienced productivity growth given that they had Malmquist Productivity Indexes greater than one.In contrast, the Malmquist Productivity Indices for 13 (56.5 per cent) hospitals were less than one, signifying productivity decline over time. None of the hospitals had Malmquist Productivity Index of exactly one, which would have signified stagnation.The average Malmquist total factor productivity (M TFP) score for the entire sample was 0.951 (STDEV=0.085); which signifies that on average hospitals experienced productivity decline between periods t and t+1 of 4.9 per cent.Whereas the relative efficiency of hospitals being assessed increased 26 per cent, technical change (innovation) regressed by 24.3per cent.Conclusion: Empirical results show evidence of a decrease in productivity among zonal public hospitals in Benin between 2003 and 2007. The decrease was largely due to technical regress.Such MTFP analyses may be useful for monitoring the effects of health sector reforms on hospital efficiency and productivity in the WHO African Region.