AIMS: To ascertain the present practices of Scottish microbiological laboratories for examining faecal samples for Cryptosporidium spp and to compare these with practices elsewhere. METHOD: A questionnaire was circulated to all 35 Scottish NHS bacteriological laboratories, where human stool samples are subjected to routine microbiological examination, to determine current laboratory testing methods and selection criteria used to examine faecal specimens for Cryptosporidium spp. RESULTS: All laboratories responded, of which the first began testing in 1984 and the last in 1990. At 15 sites all diagnostic stool samples submitted are routinely examined for Cryptosporidium spp. Elsewhere, selection criteria, principally based on age, specific request, and foreign travel, are used. The age distribution of Scottish cases differed significantly from that of the PHLS study of 16 laboratories (p < 0.001), probably as a result of the selection criteria used. The phenol-auramine staining procedure is used by 19 laboratories, with modified Ziehl-Neelsen staining used by 14 laboratories; eight used a second, confirmatory method. CONCLUSIONS: Currently applied selection criteria for examination of stools for Cryptosporidium in Scotland do not accord with published epidemiological data. Specimen selection based on age of patient and stool consistency may lead to cases of public health importance being missed. Nationally agreed criteria for testing of human samples based on epidemiological evidence are required.