Transmission electron microscopy (TEM) has been used to demonstrate the biological formation of a hollow spherical halloysite-like mineral in freshwater systems. The interaction between clays and microbes was investigated in microbial films from laboratory cultures derived from natural sediments. Optical and electron microscopic observations of cultured microbes revealed that thin clay films covered areas of the bacterial cell wall. X-ray diffraction of the thin films after 2 y of ageing showed a 7.13 Å d spacing, consistent with a 7 Å halloysite-like phase [Al2Si2O5(OH)4 · H2O]. Fourier transform infrared analysis of the thin film exhibited the characteristic adsorption bands for O–H (3651 cm−1), C–H and C–N (2925, 1454 and 1420 cm−1, respectively), suggesting that the phase was closely associated with adhesive organics. Observation by TEM of the thin films revealed that spherical, hollow, halloysite-like material formed on both coccus- and bacillus-type bacterial cells. Electron diffraction analysis of this material showed 2.9, 2.5, 2.2 and 1.5 Å d spacings. The present investigation strongly suggests that the thin film wall of the spherical halloysite-like material was associated with bacteria as a bioorganic product. This material, referred to hereafter as bio-halloysite, is further evidence for the microbially-mediated formation of clay minerals. The identity of the bacteria responsible for bio-halloysite formation is unknown, but is tentatively assigned to sulfate-reducing bacteria on the basis of morphology and the presence of reducing conditions in the microcosm at the end of the experiments.