Sequential harvests of cotton seedlings grown in soil cores enabled the quantification of the density of arbuscular mycorrhizal fungi to detect the effects of time, cultivation and periodic wetting of the soil. Cotton seedlings grown in soil cores from three locations formed arbuscular mycorrhizas at similar rates when cores were stored dry for up to 18 months. Disturbance of dry cores followed by dry storage for 18 months did not reduce the rate of establishment of mycorrhizas. Periodic wetting and drying of the cores, especially if the cores had first been disturbed, significantly reduced the rate of establishment of mycorrhizas. We suggest that long fallow disorder is possibly caused by falls of rain in clay soils of eastern Australia used to grow cotton. The proportion of the root with mycorrhizas at 3 wk was strongly correlated with the infection at 8 wk. We also suggest that it might be possible to predict maximum levels of infection and early uptake of phosphate of seedlings by determining the proportion of roots that are mycorrhizal 3 wk after emergence of cotton seedlings.