A case control study including 175 children aged 0-36 months suffering from diarrhea of > or = 14 days duration was undertaken to determine whether there is an association between Giardia lamblia, Entamoeba histolytica or Cryptosporidium infection and persistent diarrhea (PD). Subjects were identified by ongoing household surveillance and enrolled as cases. For each case two controls were selected by survey of neighbouring households--a child with acute diarrhea and one without diarrhea. Both the controls were matched with the case for age and nutritional status. Two fresh stool samples were collected from all cases and controls at enrollment and examined for trophozoites of Giardia lamblia, Entamoeba histolytica and Cryptosporidium. Giardia lamblia trophozoites were detected in a significantly higher proportion of PD cases (20.0%) than acute diarrheal and non diarrheal controls (4.6% each, p < 0.0001). There were no significant differences in the proportion of cases and controls who passed E. histolytica trophozoites or cryptosporidium in their stools. There was a consistent trend towards poorer weight gain in PD cases who passed Giardia trophozoites in stool; the differences were statistically significant at days 14 and 21, after enrollment. Giardia lamblia infection is more prevalent in PD cases than in acute diarrhea or non-diarrheal controls. This prevalence is not high enough to warrant routine anti-giardia therapy in patients with PD. However, as giardiasis was observed to have adverse growth impact in PD cases, stool microscopy for detection and subsequent treatment of Giardia lamblia seems to be justified.