Conventional diatom analysis in bioassessment does not separate live and dead diatoms in an assemblage.  We counted live diatoms (cells with chloroplasts) and compared them to the conventional method (clean counts) to assess if their relationships with the environmental variables would differ. We collected benthic diatom samples from 25 streams in the Northern Oregon Coast. A total of 149 species (135 in the clean counts and 90 in the live counts) were recorded. The mean species richness for the clean and live counts was 26 and 19, respectively. On average, the percentage of live diatoms was 63.4%. The diatom assemblages generated from the two counts were similar overall.  Their mean Bray-Curtis (BC) similarity was 77.5%. The relationships between diatom assemblages (summarized as non-metric multidimensional scaling ordination axes) and the environmental variables were similar. Both assemblages correlated well with in-stream physical habitat conditions.  Sites with the lowest BC between the two counts were small streams with low algal production. Sites with the highest BC between the two counts were bigger streams with high primary production.  In conclusion, despite relatively high proportion of dead diatoms in some diatom assemblages, their relationships with the environmental variables were similar.