ABSTRACT. – Diatom communities of Lake Balaton, the largest shallow lake of Central Europe, were studied between 2006 and 2008, with the purpose of establishing an initial database for a monitoring system for the lake in accordance with the EU Water Framework Directives. Four basins of the lake were investigated at several sampling sites; diatoms were sampled from four different substrates (reed, stone, sediment, and artificial substrates) in summer and in autumn. The goals of the investigation were to choose sampling sites, to select the most suitable substrate, and to identify an adequate index for monitoring studies of Lake Balaton in the future. 101 samples were collected and 289 diatom species were identified. The most abundant species were Achnanthidium minutissimum, Amphora pediculus, Cymbella exigua, Encyonopsis minuta, Staurosira grigorszkyi, Navicula cryptotenella and Nitzschia dissipata. Data sets were analyzed with multivariate statistical methods. Cluster analysis, Principal Component Analysis (PCA) and Self Organizing Map method indicated a clear separation between the northern and southern shore of the lake. Taking diatom samples at several sites from each shore of the lake is suggested in the future. It was shown that reed is the most suitable substrate for studying diatoms of Lake Balaton. Our results have indicated that artificial substrate is an adequate alternative, since its epiphytic diatom biota is quite similar to reed. The water quality of the lake was generally good. The Keszthely basin is the most impacted area of the lake (caused by the nutrient load of River Zala), where diatoms indicate a moderate water quality. Using IBD along with TDIL seems to be the best method of assessing the water quality of Lake Balaton.