In Scotland, rates of cryptosporidiosis infection in humans peak during the spring, a peak that is coincident with the peak in rates of infection in farm animals (during lambing and calving time). Here we show that, during the outbreak of foot and mouth disease (FMD) in 2001, there was a significant reduction in human cases of cryptosporidiosis infection in southern Scotland, where FMD was present, whereas, in the rest of Scotland, there was a reduction in cases that was not significant. We associate the reduction in human cases of cryptosporidiosis infection with the reduction in the number of young farm animals, together with restrictions on movement of both farm animals and humans, during the outbreak of FMD in 2001. We further show that, during 2002, there was recovery in the rate of cryptosporidiosis infection in humans throughout Scotland, particularly in the FMD-infected area, but that rates of infection remained lower, though not significantly, than pre-2001 levels.