Abstract Information on functional diversity (metabolic potential) is essential for understanding the role of microbial communities in different environments. Variations of the commercially available BIOLOG bacterial identification system plates are now widely used to assess functional diversity of microorganisms from environmental samples, based on utilisation patterns of a wide range (up to 95) of single carbon sources. There are many problems as well as benefits of using the approach, but the former are often disregarded. Here the basis of the approach is summarised, including type of plate to use, treatment of samples, replication, incubation conditions, monitoring of plates, and statistical analysis. The pros and cons of its use are critically assessed, inherent biases and limitations are pointed out and methodological difficulties are considered. Possible ways of overcoming some of the difficulties are suggested.