Coccidial infections were studied in goats in the state of Selangor (peninsular Malaysia) during a 12-month period. The study included 10 smallholder farms on which kids were monitored for faecal oocyst counts from birth until 1-year old. Eimeria oocysts were found in 725 (89%) of 815 faecal samples examined. Nine species of Eimeria were identified. The most prevalent were E. arloingi, found in 71% of the samples, E. ninakohlyakimovae (67%), E. christenseni (63%) and E. alijevi (61%). The other species found were, E. hirci, E. jolchijevi, E. caprovina, E. caprina and E. pallida, present in 34, 22, 12, 9 and 4% of the samples, respectively. Oocyst counts were significantly higher in animals of less than 4-months old (P < 0.05). High oocyst counts were mainly caused by non-pathogenic species. Poor hygienic conditions were found to be associated with a higher intensity of coccidial infections. Mortality rates in kids could not be related to the intensity of coccidial infections.