The environmental release of genetically engineered (transgenic) plants may be accompanied by ecological effects including changes in the plant-associated microflora. A field release of transgenic potato plants that produce the insecticidal endotoxin of Bacillus thuringiensis var. tenebrionis (Bit) was monitored for changes in total bacterial and fungal populations, fungal species diversity and abundance, and plant pathogen levels. The microflora on three phenological stages of leaves (green, yellow and brown) were compared over the growing season (sample days 0, 21, 42, 63 and 98) for transgenic potato plants, commercial Russet Burbank potato plants treated with systemic insecticide (Di-Syston) and commercial Russet Burbank potato plants treated with microbial Btt (M-Trak). In addition, plant and soil assays were performed to assess disease incidence of Fusarium spp., Pythium spp., Verticillium dahliae, potato leaf roll virus (PLRV) and potato virus Y (PVY). Few significant differences in phylloplane microflora among the plant types were observed and none of the differences were persistent. Total bacterial populations on brown leaves on sample day 21 and on green leaves on sample day 42 were significantly higher on the transgenic potato plants. Total fungal populations on green leaves on sample day 63 were significantly different among the three plant types; lowest levels were on the commercial potato plants treated with systemic insecticide and highest levels were on the commercial potato plants treated with microbial Btt. Differences in fungal species assemblages and diversity were correlated with sampling dates, but relatively consistent among treatments. Alternaria alternata, a common saprophyte on leaves and in soil and leaf litter, was the most commonly isolated fungus species for all the plant treatments. Rhizosphere populations of the soilborne pathogens Pythium spp., Fusarium spp. and V. dahliae did not differ between the transgenic potato plants and the commercial potato plants treated with systemic insecticide. The incidence of tuber infection at the end of the growing season by the plant pathogen V. dahliae was highest for the transgenic potato plants but this difference was related to longer viability of the transgenic potato plants. This difference in longevity between the transgenic potato plants and the commercial + systemic insecticide potato plants also made comparison of the incidence of PVY and PLRV problematic. Our results indicate that under field conditions the microflora of transgenic Btt-producing potato plants differed minimally from that of chemically and microbially treated commercial potato plants.