Studies of intestinal helminth infections are influenced by the constraints of sample collection, as identification of helminth ova in stools is affected by the time since evacuation from the host. Different methods may be required to optimise diagnostic sensitivity under different study conditions. In the context of studies in rural Malawi, we collected stool samples with different time delays from production by subjects to sample collection by field staff, to examination in the laboratory. Stools were processed by Kato-Katz (KK) or formol-ether concentration (FEC) methods. Hookworm and Schistosoma mansoni were the most common helminths identified. The prevalence of hookworm was higher with KK (270/988, 27%) than with FEC (191/988, 19%). Comparison was made between the results from the two methods according to the timing of the processing steps. Delays in processing did not affect retrieval of S. mansoni. A decrease in sensitivity of almost 50% for detection of hookworm was observed with either method when preservation/refrigeration was delayed by more than 3h. A delay of 1 day from refrigeration or preservation to laboratory processing also reduced the sensitivity for hookworm by 50% for both methods. Care must be taken in studies of multiple helminth infections owing to the selective reduction of hookworm ova during transport. This is particularly critical when samples are not preserved, even over short periods of time, and even with formalin preservation.