BACKGROUND The purpose of this study was to investigate the effect of anthropometric characteristics and training indices on marathon race times in recreational male marathoners. METHODS Training and anthropometric characteristics were collected for a large cohort of recreational male runners (n = 126) participating in the Basel marathon in Switzerland between 2010 and 2011. RESULTS Among the parameters investigated, marathon performance time was found to be affected by mean running speed and the mean weekly distance run during the training period prior to the race and by body fat percentage. The effect of body fat percentage became significant as it exceeded a certain limiting value; for a relatively low body fat percentage, marathon performance time correlated only with training indices. CONCLUSIONS Marathon race time may be predicted (r = 0.81) for recreational male runners by the following equation: marathon race time (minutes) = 11.03 + 98.46 exp(-0.0053 mean weekly training distance [km/week]) + 0.387 mean training pace (sec/km) + 0.1 exp(0.23 body fat percentage [%]). The marathon race time results were valid over a range of 165-266 minutes.