The Invertebrate Data Analysis System (IDAS) software was developed to provide an accurate, consistent, and efficient mechanism for analyzing invertebrate data collected as part of the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program. The IDAS software is a stand-alone program for personal computers that run Microsoft Windows(Registered). It allows users to read data downloaded from the NAWQA Program Biological Transactional Database (Bio-TDB) or to import data from other sources either as Microsoft Excel(Registered) or Microsoft Access(Registered) files. The program consists of five modules: Edit Data, Data Preparation, Calculate Community Metrics, Calculate Diversities and Similarities, and Data Export. The Edit Data module allows the user to subset data on the basis of taxonomy or sample type, extract a random subsample of data, combine or delete data, summarize distributions, resolve ambiguous taxa (see glossary) and conditional/provisional taxa, import non-NAWQA data, and maintain and create files of invertebrate attributes that are used in the calculation of invertebrate metrics. The Data Preparation module allows the user to select the type(s) of sample(s) to process, calculate densities, delete taxa on the basis of laboratory processing notes, delete pupae or terrestrial adults, combine lifestages or keep them separate, select a lowest taxonomic level for analysis, delete rare taxa on the basis of the number of sites where a taxon occurs and (or) the abundance of a taxon in a sample, and resolve taxonomic ambiguities by one of four methods. The Calculate Community Metrics module allows the user to calculate 184 community metrics, including metrics based on organism tolerances, functional feeding groups, and behavior. The Calculate Diversities and Similarities module allows the user to calculate nine diversity and eight similarity indices. The Data Export module allows the user to export data to other software packages (CANOCO, Primer, PC-ORD, MVSP) and produce tables of community data that can be imported into spreadsheet, database, graphics, statistics, and word-processing programs. The IDAS program facilitates the documentation of analyses by keeping a log of the data that are processed, the files that are generated, and the program settings used to process the data. Though the IDAS program was developed to process NAWQA Program invertebrate data downloaded from Bio-TDB, the Edit Data module includes tools that can be used to convert non-NAWQA data into Bio-TDB format. Consequently, the data manipulation, analysis, and export procedures provided by the IDAS program can be used to process data generated outside of the NAWQA Program.