Globally, diarrhoeal disease is among the leading cause of mortality and morbidity among children aged five years and below. In developing countries, children living in poor areas with unsafe water supplies and inadequate levels of hygiene and sanitation conditions are most at risk of developing persistent diarrhoea. Besides the enteric viruses and bacteria, intestinal protozoan parasites including Cryptosporidium spp. and Giardia spp. have also been recognised as the important causes of diarrhoeal disease. They can be transmitted by person to person via faecal-oral route or indirect route through contaminated food and drinking water with human or animal faeces. Most infections are self-limited but recurrences are common in endemic areas. However, chronic infection can lead to weight loss, malnutrition, cognitive impairment and potentially life-threatening in immunocompromised children. Given the importance of intestinal parasite as a cause of paediatric diarrhoeal disease, further studies targeting sociodemographic characteristics, behavioral and hygienic practice status are required. Adequate knowledge of the molecular diversity and geographical distribution of these parasites and the environmental and climatic variables that influence their prevalence will enable the implementation of multiple intervention strategies for children, households and their environments to combat preventable morbidity and mortality from diarrhoeal diseases.