Negative staining technique of Heine is an easy, inexpensive, and rapid way of screening for coccidian parasites of the intestinal tract. But its use as a routine technique for screening of Cryptosporidium, Cyclospora, and Cystoisospora is restricted due to its sensitivity being lower than the gold standard method of modified Ziehl-Neelsen staining. This paper emphasises the modification of original Heine staining technique which has been attempted in order to increase the sensitivity and detection of oocysts of Cryptosporidium, Cyclospora, and Cystoisospora. Modified Heine staining technique using malachite green is a practical, safe, and sensitive method of detecting oocysts in stool specimens. While the modified Ziehl-Neelsen staining technique is still considered the gold standard for the detection of Cryptosporidium spp., modified negative staining technique of Heine using malachite green stain should be considered as the screening technique of first choice.