In this study, the performance of the MicroFoss system (Foss, Spain) for the enumeration of Escherichia coli in water samples was evaluated. One hundred and eighty-five samples were analysed both by MicroFoss assay and culture isolation on Tryptone-Bile X-glucuronide agar (TBX), and the correlation coefficient obtained was 0.92. The analysis of 28 new samples using both methods showed a statistically significant relationship at the 99.5% confidence level between log colony forming units obtained by MicroFoss assay and those obtained using growth on TBX agar. Nevertheless, when the level of sample contamination was low, the variability was high. In conclusion, the MicroFoss system is a rapid and simple alternative method for the enumeration of E. coli in water although discordance between the results using these methods in samples with low counts could limit its use for the study of clean water such as potable water.